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AuthorTitleYearJournal/ProceedingsReftypeDOI/URL
Vaitkus, A., Merkys, A., Sander, T., Quirós, M., Thiessen, P.A., Bolton, E.E. and Gražulis, S. A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database 2023 J. Cheminf.
Vol. 15(1) 
article DOI  
BibTeX:
@article{Vaitkus2023,
  author = {Vaitkus, Antanas and Merkys, Andrius and Sander, Thomas and Quirós, Miguel and Thiessen, Paul A. and Bolton, Evan E. and Gražulis, Saulius},
  title = {A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database},
  journal = {J. Cheminf.},
  publisher = {Springer Science and Business Media LLC},
  year = {2023},
  volume = {15},
  number = {1},
  doi = {https://doi.org/10.1186/s13321-023-00780-2}
}
Lingė, D., Gedgaudas, M., Merkys, A., Petrauskas, V., Vaitkus, A., Grybauskas, A., Paketurytė, V., Zubrienė, A., Zakšauskas, A., Mickevičiūtė, A., Smirnovienė, J., Baranauskienė, L., Čapkauskaitė, E., Dudutienė, V., Urniežius, E., Konovalovas, A., Kazlauskas, E., Shubin, K., Schiöth, H.B., Chen, W.-Y., Ladbury, J.E., Gražulis, S. and Matulis, D. PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters 2023 Database
Vol. 2023 
article DOI  
BibTeX:
@article{Linge2023,
  author = {Darius Lingė and Marius Gedgaudas and Andrius Merkys and Vytautas Petrauskas and Antanas Vaitkus and Algirdas Grybauskas and Vaida Paketurytė and Asta Zubrienė and Audrius Zakšauskas and Aurelija Mickevičiūtė and Joana Smirnovienė and Lina Baranauskienė and Edita Čapkauskaitė and Virginija Dudutienė and Ernestas Urniežius and Aleksandras Konovalovas and Egidijus Kazlauskas and Kirill Shubin and Helgi B. Schiöth and Wen-Yih Chen and John E. Ladbury and Saulius Gražulis and Daumantas Matulis},
  title = {PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters},
  journal = {Database},
  publisher = {Oxford University Press (OUP)},
  year = {2023},
  volume = {2023},
  doi = {https://doi.org/10.1093/database/baad040}
}
Manakova, E., Golovinas, E., Pocevičiűtė, R., Sasnauskas, G., Grybauskas, A., Gražulis, S. and Zaremba, M. Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein 2023 Sci. Rep.
Vol. 13(1), pp. 6123 
article DOI  
BibTeX:
@article{Manakova2023,
  author = {Elena Manakova and Edvardas Golovinas and Reda Pocevičiűtė and Giedrius Sasnauskas and Algirdas Grybauskas and Saulius Gražulis and Mindaugas Zaremba},
  title = {Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein},
  journal = {Sci. Rep.},
  publisher = {Springer Science and Business Media LLC},
  year = {2023},
  volume = {13},
  number = {1},
  pages = {6123},
  doi = {https://doi.org/10.1038/s41598-023-32600-w}
}
Balandis, B., Šimkūnas, T., Paketurytė-Latvė, V., Michailovienė, V., Mickevičiūtė, A., Manakova, E., Gražulis, S., Belyakov, S., Kairys, V., Mickevičius, V., Zubrienė, A. and Matulis, D. Beta and gamma amino acid-substituted benzenesulfonamides as inhibitors of human carbonic anhydrases 2022 Pharmaceuticals
Vol. 15(4), pp. 477 
article DOI  
BibTeX:
@article{Balandis2022,
  author = {Benas Balandis and Tomas Šimkūnas and Vaida Paketurytė-Latvė and Vilma Michailovienė and Aurelija Mickevičiūtė and Elena Manakova and Saulius Gražulis and Sergey Belyakov and Visvaldas Kairys and Vytautas Mickevičius and Asta Zubrienė and Daumantas Matulis},
  title = {Beta and gamma amino acid-substituted benzenesulfonamides as inhibitors of human carbonic anhydrases},
  journal = {Pharmaceuticals},
  publisher = {MDPI AG},
  year = {2022},
  volume = {15},
  number = {4},
  pages = {477},
  doi = {https://doi.org/10.3390/ph15040477}
}
Merkys, A., Vaitkus, A., Grybauskas, A., Konovalovas, A., Quirós, M. and Gražulis, S. Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions 2023 J. Cheminf.
Vol. 15(1) 
article DOI  
BibTeX:
@article{Merkys2023,
  author = {Andrius Merkys and Antanas Vaitkus and Algirdas Grybauskas and Aleksandras Konovalovas and Miguel Quirós and Saulius Gražulis},
  title = {Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions},
  journal = {J. Cheminf.},
  publisher = {Springer Science and Business Media LLC},
  year = {2023},
  volume = {15},
  number = {1},
  doi = {https://doi.org/10.1186/s13321-023-00692-1}
}
Jozeliūnaitė, A., Rahmanudin, A., Gražulis, S., Baudat, E., Sivula, K., Fazzi, D., Orentas, E. and Sforazzini, G. Light-responsive oligothiophenes incorporating photochromic torsional switches 2022 Chemistry – A European Journal  article DOI  
BibTeX:
@article{Jozeliunaite2022,
  author = {Augustina Jozeliūnaitė and Aiman Rahmanudin and Saulius Gražulis and Emilie Baudat and Kevin Sivula and Daniele Fazzi and Edvinas Orentas and Giuseppe Sforazzini},
  title = {Light-responsive oligothiophenes incorporating photochromic torsional switches},
  journal = {Chemistry – A European Journal},
  publisher = {Wiley},
  year = {2022},
  doi = {https://doi.org/10.1002/chem.202202698}
}
Petrauskas, K., Merkys, A., Vaitkus, A., Laibinis, L. and Gražulis, S. Proving the correctness of the algorithm for building a crystallographic space group 2022 J. Appl. Crystallogr.
Vol. 55(3), pp. 515-525 
article DOI URL 
BibTeX:
@article{Petrauskas2022,
  author = {Karolis Petrauskas and Andrius Merkys and Antanas Vaitkus and Linas Laibinis and Saulius Gražulis},
  title = {Proving the correctness of the algorithm for building a crystallographic space group},
  journal = {J. Appl. Crystallogr.},
  publisher = {International Union of Crystallography (IUCr)},
  year = {2022},
  volume = {55},
  number = {3},
  pages = {515--525},
  doi = {https://doi.org/10.1107/s1600576722003107}
}
Andersen, C.W., Armiento, R., Blokhin, E., Conduit, G.J., Dwaraknath, S., Evans, M.L., Fekete, Á., Gopakumar, A., Gražulis, S., Merkys, A., Mohamed, F., Oses, C., Pizzi, G., Rignanese, G.-M., Scheidgen, M., Talirz, L., Toher, C., Winston, D., Aversa, R., Choudhary, K., Colinet, P., Curtarolo, S., Stefano, D.D., Draxl, C., Er, S., Esters, M., Fornari, M., Giantomassi, M., Govoni, M., Hautier, G., Hegde, V., Horton, M.K., Huck, P., Huhs, G., Hummelshøj, J., Kariryaa, A., Kozinsky, B., Kumbhar, S., Liu, M., Marzari, N., Morris, A.J., Mostofi, A.A., Persson, K.A., Petretto, G., Purcell, T., Ricci, F., Rose, F., Scheffler, M., Speckhard, D., Uhrin, M., Vaitkus, A., Villars, P., Waroquiers, D., Wolverton, C., Wu, M. and Yang, X. OPTIMADE, an API for exchanging materials data 2021 Sci. Data
Vol. 8(1) 
article DOI  
BibTeX:
@article{Andersen2021,
  author = {Casper W. Andersen and Rickard Armiento and Evgeny Blokhin and Gareth J. Conduit and Shyam Dwaraknath and Matthew L. Evans and Ádám Fekete and Abhijith Gopakumar and Saulius Gražulis and Andrius Merkys and Fawzi Mohamed and Corey Oses and Giovanni Pizzi and Gian-Marco Rignanese and Markus Scheidgen and Leopold Talirz and Cormac Toher and Donald Winston and Rossella Aversa and Kamal Choudhary and Pauline Colinet and Stefano Curtarolo and Davide Di Stefano and Claudia Draxl and Suleyman Er and Marco Esters and Marco Fornari and Matteo Giantomassi and Marco Govoni and Geoffroy Hautier and Vinay Hegde and Matthew K. Horton and Patrick Huck and Georg Huhs and Jens Hummelshøj and Ankit Kariryaa and Boris Kozinsky and Snehal Kumbhar and Mohan Liu and Nicola Marzari and Andrew J. Morris and Arash A. Mostofi and Kristin A. Persson and Guido Petretto and Thomas Purcell and Francesco Ricci and Frisco Rose and Matthias Scheffler and Daniel Speckhard and Martin Uhrin and Antanas Vaitkus and Pierre Villars and David Waroquiers and Chris Wolverton and Michael Wu and Xiaoyu Yang},
  title = {OPTIMADE, an API for exchanging materials data},
  journal = {Sci. Data},
  publisher = {Springer Science and Business Media LLC},
  year = {2021},
  volume = {8},
  number = {1},
  doi = {https://doi.org/10.1038/s41597-021-00974-z}
}
Smirnovienė, J., Smirnov, A., Zakšauskas, A., Zubrienė, A., Petrauskas, V., Mickevičiūtė, A., Michailovienė, V., Čapkauskaitė, E., Manakova, E., Gražulis, S., Baranauskienė, L., Chen, W.-Y., Ladbury, J.E. and Matulis, D. Switching the inhibitor-enzyme recognition profile via chimeric Carbonic anhydrase XII 2021 ChemistryOpen
Vol. 10(5), pp. 567-580 
article DOI  
BibTeX:
@article{Smirnoviene2021,
  author = {Joana Smirnovienė and Alexey Smirnov and Audrius Zakšauskas and Asta Zubrienė and Vytautas Petrauskas and Aurelija Mickevičiūtė and Vilma Michailovienė and Edita Čapkauskaitė and Elena Manakova and Saulius Gražulis and Lina Baranauskienė and Wen-Yih Chen and John E. Ladbury and Daumantas Matulis},
  title = {Switching the inhibitor-enzyme recognition profile via chimeric Carbonic anhydrase XII},
  journal = {ChemistryOpen},
  publisher = {Wiley},
  year = {2021},
  volume = {10},
  number = {5},
  pages = {567--580},
  doi = {https://doi.org/10.1002/open.202100042}
}
Vaitkus, A., Merkys, A. and Gražulis, S. Validation of the Crystallography Open Database using the Crystallographic Information Framework 2021 J. Appl. Crystallogr.
Vol. 54(2), pp. 661-672 
article DOI  
BibTeX:
@article{Vaitkus2021,
  author = {Antanas Vaitkus and Andrius Merkys and Saulius Gražulis},
  title = {Validation of the Crystallography Open Database using the Crystallographic Information Framework},
  journal = {J. Appl. Crystallogr.},
  publisher = {International Union of Crystallography (IUCr)},
  year = {2021},
  volume = {54},
  number = {2},
  pages = {661--672},
  doi = {https://doi.org/10.1107/s1600576720016532}
}
Mickevičiūtė, A., Timm, D.D., Gedgaudas, M., Linkuvienė, V., Chen, Z., Waheed, A., Michailovienė, V., Zubrienė, A., Smirnov, A., Čapkauskaitė, E., Baranauskienė, L., Jachno, J., Revuckienė, J., Manakova, E., Gražulis, S., Matulienė, J., Cera, E.D., Sly, W.S. and Matulis, D. Intrinsic thermodynamics of high affinity inhibitor binding to recombinant human carbonic anhydrase IV 2017 Eur. Biophys. J.
Vol. 47(3), pp. 271-290 
article DOI  
BibTeX:
@article{Mickeviciute2017,
  author = {Aurelija Mickevičiūtė and David D. Timm and Marius Gedgaudas and Vaida Linkuvienė and Zhiwei Chen and Abdul Waheed and Vilma Michailovienė and Asta Zubrienė and Alexey Smirnov and Edita Čapkauskaitė and Lina Baranauskienė and Jelena Jachno and Jurgita Revuckienė and Elena Manakova and Saulius Gražulis and Jurgita Matulienė and Enrico Di Cera and William S. Sly and Daumantas Matulis},
  title = {Intrinsic thermodynamics of high affinity inhibitor binding to recombinant human carbonic anhydrase IV},
  journal = {Eur. Biophys. J.},
  publisher = {Springer Nature},
  year = {2017},
  volume = {47},
  number = {3},
  pages = {271--290},
  doi = {https://doi.org/10.1007/s00249-017-1256-0}
}
Fuentes-Cobas, L.E., Chateigner, D., Fuentes-Montero, M.E., Pepponi, G. and Grazulis, S. The representation of coupling interactions in the Material Properties Open Database (MPOD) 2017 Adv. Appl. Ceram.
Vol. 116(8), pp. 428-433 
article DOI  
BibTeX:
@article{Fuentes-Cobas2017,
  author = {Luis E. Fuentes-Cobas and Daniel Chateigner and Mar\ia E. Fuentes-Montero and Giancarlo Pepponi and Saulius Grazulis},
  title = {The representation of coupling interactions in the Material Properties Open Database (MPOD)},
  journal = {Adv. Appl. Ceram.},
  publisher = {Informa UK Limited},
  year = {2017},
  volume = {116},
  number = {8},
  pages = {428--433},
  doi = {https://doi.org/10.1080/17436753.2017.1343782}
}
Gražulis, S., Merkys, A., Vaitkus, A., Chateigner, D., Lutterotti, L., Moeck, P., Quiros, M., Downs, R.T., Kaminsky, W. and Le Bail, A. Crystallography open database: history, development, and perspectives 2019 Materials Informatics, pp. 1-39  book DOI URL 
BibTeX:
@book{Grazulis2019,
  author = {Gražulis, Saulius and Merkys, A. and Vaitkus, A. and Chateigner, D. and Lutterotti, L. and Moeck, P. and Quiros, M. and Downs, R. T. and Kaminsky, W. and Le Bail, A.},
  title = {Crystallography open database: history, development, and perspectives},
  booktitle = {Materials Informatics},
  publisher = {Wiley},
  year = {2019},
  pages = {1--39},
  url = {https://doi.org/10.1002/9783527802265.ch1},
  doi = {https://doi.org/10.1002/9783527802265.ch1}
}
Smirnov, A., Manakova, E., Gražulis, S., McKenna, R. and Matulis, D. Structures of carbonic anhydrases and their complexes with inhibitors 2019 Carbonic anhydrase as drug targets  book URL 
BibTeX:
@book{Smirnov2019,
  author = {Smirnov, A. and Manakova, E. and Gražulis, Saulius and McKenna, R. and Matulis, D.},
  title = {Structures of carbonic anhydrases and their complexes with inhibitors},
  booktitle = {Carbonic anhydrase as drug targets},
  publisher = {Springer},
  year = {2019},
  url = {https://tinyurl.com/y5hqomv8}
}
Smirnov, A., Zubrienė, A., Manakova, E., Gražulis, S. and Matulis, D. Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding 2018 PeerJ
Vol. 6, pp. e4412 
article DOI  
BibTeX:
@article{Smirnov2018,
  author = {Alexey Smirnov and Asta Zubrienė and Elena Manakova and Saulius Gražulis and Daumantas Matulis},
  title = {Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding},
  journal = {PeerJ},
  publisher = {PeerJ},
  year = {2018},
  volume = {6},
  pages = {e4412},
  doi = {https://doi.org/10.7717/peerj.4412}
}
Mendili, Y.E., Vaitkus, A., Merkys, A., Gražulis, S., Chateigner, D., Mathevet, F., Gascoin, S., Petit, S., Bardeau, J.-F., Zanatta, M., Secchi, M., Mariotto, G., Kumar, A., Cassetta, M., Lutterotti, L., Borovin, E., Orberger, B., Simon, P., Hehlen, B. and Guen, M.L. Raman Open Database: first interconnected Raman–X-ray diffraction open-access resource for material identification 2019 J. Appl. Crystallogr.
Vol. 52(3), pp. 618-625 
article DOI  
BibTeX:
@article{Mendili2019,
  author = {Yassine El Mendili and Antanas Vaitkus and Andrius Merkys and Saulius Gražulis and Daniel Chateigner and Fabrice Mathevet and Stéphanie Gascoin and Sebastien Petit and Jean-François Bardeau and Marco Zanatta and Maria Secchi and Gino Mariotto and Arun Kumar and Michele Cassetta and Luca Lutterotti and Evgeny Borovin and Beate Orberger and Patrick Simon and Bernard Hehlen and Monique Le Guen},
  title = {Raman Open Database: first interconnected Raman–X-ray diffraction open-access resource for material identification},
  journal = {J. Appl. Crystallogr.},
  publisher = {International Union of Crystallography (IUCr)},
  year = {2019},
  volume = {52},
  number = {3},
  pages = {618--625},
  doi = {https://doi.org/10.1107/s1600576719004229}
}
Gražulis, S., Merkys, A. and Vaitkus, A. Crystallography Open Database (COD) 2018 Handbook of Materials Modeling, pp. 1-19  book DOI  
BibTeX:
@book{Grazulis2018,
  author = {Saulius Gražulis and Andrius Merkys and Antanas Vaitkus},
  title = {Crystallography Open Database (COD)},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  year = {2018},
  pages = {1--19},
  doi = {https://doi.org/10.1007/978-3-319-42913-7_66-1}
}
Quirós, M., Gražulis, S., Girdzijauskaitė, S., Merkys, A. and Vaitkus, A. Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database 2018 J. Cheminf.  article DOI URL 
BibTeX:
@article{Quiros2018,
  author = {Miguel Quirós and Saulius Gražulis and Saulė Girdzijauskaitė and Andrius Merkys and Antanas Vaitkus},
  title = {Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database},
  journal = {J. Cheminf.},
  year = {2018},
  url = {http://doi.org/10.1186/s13321-018-0279-6},
  doi = {https://doi.org/10.1186/s13321-018-0279-6}
}
Tamulaitienė, G., Manakova, E., Jovaišaitė, V., Tamulaitis, G., Gražulis, S., Bochtler, M. and Šikšnys, V. Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family 2018 Nucleic Acids Res., pp. 997-1010  article DOI  
BibTeX:
@article{Tamulaitiene2018,
  author = {Giedrė Tamulaitienė and Elena Manakova and Virginija Jovaišaitė and Gintautas Tamulaitis and Saulius Gražulis and Matthias Bochtler and Virginijus Šikšnys},
  title = {Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family},
  journal = {Nucleic Acids Res.},
  publisher = {Oxford University Press (OUP)},
  year = {2018},
  pages = {997--1010},
  doi = {https://doi.org/10.1093/nar/gky1137}
}
Tamulaitis, G., Rutkauskas, M., Zaremba, M., Gražulis, S., Tamulaitienė, G. and Šikšnys, V. Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI 2015 Nucleic Acids Res.
Vol. 43(16), pp. 8100-8110 
article DOI  
BibTeX:
@article{Tamulaitis2015,
  author = {Gintautas Tamulaitis and Marius Rutkauskas and Mindaugas Zaremba and Saulius Gražulis and Giedrė Tamulaitienė and Virginijus Šikšnys},
  title = {Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI},
  journal = {Nucleic Acids Res.},
  publisher = {Oxford University Press (OUP)},
  year = {2015},
  volume = {43},
  number = {16},
  pages = {8100--8110},
  doi = {https://doi.org/10.1093/nar/gkv768}
}
Bruno, I., Gražulis, S., Helliwell, J.R., Kabekkodu, S.N., McMahon, B. and Westbrook, J. Crystallography and databases 2017 Data Sci. J.
Vol. 16, pp. 38 
article DOI  
BibTeX:
@article{Bruno2017,
  author = {Ian Bruno and Saulius Gražulis and John R Helliwell and Soorya N Kabekkodu and Brian McMahon and John Westbrook},
  title = {Crystallography and databases},
  journal = {Data Sci. J.},
  publisher = {Ubiquity Press, Ltd.},
  year = {2017},
  volume = {16},
  pages = {38},
  doi = {https://doi.org/10.5334/dsj-2017-038}
}
Merkys, A., Mounet, N., Cepellotti, A., Marzari, N., Gražulis, S. and Pizzi, G. A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD 2017 J. Cheminf.
Vol. 9(1), pp. 56 
article DOI  
BibTeX:
@article{Merkys2017,
  author = {Andrius Merkys and Nicolas Mounet and Andrea Cepellotti and Nicola Marzari and Saulius Gražulis and Giovanni Pizzi},
  title = {A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD},
  journal = {J. Cheminf.},
  publisher = {Springer Nature},
  year = {2017},
  volume = {9},
  number = {1},
  pages = {56},
  doi = {https://doi.org/10.1186/s13321-017-0242-y}
}
Tamulaitienė, G., Jovaišaitė, V., Tamulaitis, G., Songailiene, I., Manakova, E., Zaremba, M., Gražulis, S., Xu, S.-y. and Šikšnys, V. Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA 2016 Nucleic Acids Res., pp. 3547-3558  article DOI URL 
BibTeX:
@article{Tamulaitiene2016,
  author = {Tamulaitienė, Giedrė and Jovaišaitė, Virginija and Tamulaitis, Gintautas and Songailiene, Inga and Manakova, Elena and Zaremba, Mindaugas and Gražulis, Saulius and Xu, Shuang-yong and Šikšnys, Virginijus},
  title = {Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA},
  journal = {Nucleic Acids Res.},
  publisher = {Oxford University Press (OUP)},
  year = {2016},
  pages = {3547--3558},
  url = {http://dx.doi.org/10.1093/nar/gkw1310},
  doi = {https://doi.org/10.1093/nar/gkw1310}
}
Long, F., Nicholls, R.A., Emsley, P., Gražulis, S., Merkys, A., Vaitkus, A. and Murshudov, G.N. ACEDRG: A stereo-chemical description generator for ligands 2017 Acta Crystallogr. D
Vol. 73(2), pp. 112-122 
article DOI  
Abstract: The program AceDRG is designed for the derivation of stereochemical
information about small molecules. It uses local chemical and topological
environment-based atom typing to derive and organize bond lengths
and angles from a small-molecule database: the Crystallography Open
Database (COD). Information about the hybridization states of atoms,
whether they belong to small rings (up to seven-membered rings),
ring aromaticity and nearest- neighbour information is encoded in
the atom types. All atoms from COD have been classified according
to the generated atom types. All bonds and angles have also been
classified according to the atom types and, in a certain sense, bond
types. Derived data are tabulated in a machine-readable form that
is freely available from CCP4. AceDRG can also generate stereochemical
information, provided that the basic bonding pattern of a ligand
is known. The basic bonding pattern is perceived from one of the
computational chemistry file formats, including SMILES, mmCIF, SDF
MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types,
and bond and angle tables generated from COD, AceDRG derives the
‘ideal’ bond lengths, angles, plane groups, aromatic rings and chirality
information, and writes them to an mmCIF file that can be used by
the refinement program REFMAC5 and the model-building program Coot.
Other refinement and model-building programs such as PHENIX and BUSTER
can also use these files. AceDRG also generates one or more coordinate
sets corresponding to the most favourable conformation(s) of a given
ligand. AceDRG employs RDKit for chemistry perception and for initial
conformation generation, as well as for the interpretation of SMILES
strings, SDF MOL and SYBYL MOL2 files.
BibTeX:
@article{Long2017,
  author = {Fei Long and Robert A. Nicholls and Paul Emsley and Saulius Gražulis and Andrius Merkys and Antanas Vaitkus and Garib N. Murshudov},
  title = {ACEDRG: A stereo-chemical description generator for ligands},
  journal = {Acta Crystallogr. D},
  year = {2017},
  volume = {73},
  number = {2},
  pages = {112--122},
  doi = {https://doi.org/10.1107/S2059798317000067}
}
Long, F., Nicholls, R.A., Emsley, P., Gražulis, S., Merkys, A., Vaitkus, A. and Murshudov, G.N. Validation and extraction of stereochemical information from small molecular databases 2017 Acta Crystallogr. D
Vol. 73(2), pp. 103-111 
article DOI  
Abstract: A freely available small-molecule structure database, the Crystallography
Open Database (COD), is used for the extraction of molecular-geometry
information on small-molecule compounds. The results are used for
the generation of new ligand descriptions, which are subsequently
used by macromolecular model- building and structure-refinement software.
To increase the reliability of the derived data, and therefore the
new ligand descriptions, the entries from this database were subjected
to very strict validation. The selection criteria made sure that
the crystal structures used to derive atom types, bond and angle
classes are of sufficiently high quality. Any suspicious entries
at a crystal or molecular level were removed from further consideration.
The selection criteria included (i) the resolution of the data used
for refinement (entries solved at 0.84 A resolution or higher) and
(ii) the structure-solution method (structures must be from a single-crystal
experiment and all atoms of generated molecules must have full occupancies),
as well as basic sanity checks such as (iii) consistency between
the valences and the number of connections between atoms, (iv) acceptable
bond-length deviations from the expected values and (v) detection
of atomic collisions. The derived atom types and bond classes were
then validated using high-order moment-based statistical techniques.
The results of the statistical analyses were fed back to fine-tune
the atom typing. The developed procedure was repeated four times,
resulting in fine-grained atom typing, bond and angle classes. The
procedure will be repeated in the future as and when new entries
are deposited in the COD. The whole procedure can also be applied
to any source of small-molecule structures, including the Cambridge
Structural Database and the ZINC database.
BibTeX:
@article{Long2017a,
  author = {Fei Long and Robert A. Nicholls and Paul Emsley and Saulius Gražulis and Andrius Merkys and Antanas Vaitkus and Garib N. Murshudov},
  title = {Validation and extraction of stereochemical information from small molecular databases},
  journal = {Acta Crystallogr. D},
  year = {2017},
  volume = {73},
  number = {2},
  pages = {103-111},
  doi = {https://doi.org/10.1107/S2059798317000079}
}
Gražulis, S., Sarjeant, A.A., Moeck, P., Stone-Sundberg, J., Snyder, T.J., Kaminsky, W., Oliver, A.G., Stern, C.L., Dawe, L.N., Rychkov, D.A., Losev, E.A., Boldyreva, E.V., Tanski, J.M., Bernstein, J., Rabeh, W.M. and Kantardjieff, K.A. Crystallographic education in the 21st century 2015 J. Appl. Crystallogr.
Vol. 48(6), pp. 1964-1975 
article DOI URL 
Abstract: There are many methods that can be used to incorporate concepts of
crystallography into the learning experiences of students, whether
they are in elementary school, at university or part of the public
at large. It is not always critical that those who teach crystallography
have immediate access to diffraction equipment to be able to introduce
the concepts of symmetry, packing or molecular structure in an age-
and audience-appropriate manner. Crystallography can be used as a
tool for teaching general chemistry concepts as well as general research
techniques without ever having a student determine a crystal structure.
Thus, methods for younger students to perform crystal growth experiments
of simple inorganic salts, organic compounds and even metals are
presented. For settings where crystallographic instrumentation is
accessible (proximally or remotely), students can be involved in
all steps of the process, from crystal growth, to data collection,
through structure solution and refinement, to final publication.
Several approaches based on the presentations in the MS92 Microsymposium
at the IUCr 23rd Congress and General Assembly are reported. The
topics cover methods for introducing crystallography to undergraduate
students as part of a core chemistry curriculum; a successful short-course
workshop intended to bootstrap researchers who rely on crystallography
for their work; and efforts to bring crystallography to secondary
school children and non-science majors. In addition to these workshops,
demonstrations and long-format courses, open-format crystallographic
databases and three-dimensional printed models as tools that can
be used to excite target audiences and inspire them to pursue a deeper
understanding of crystallography are described.
BibTeX:
@article{Grazulis2015b,
  author = {Gražulis, Saulius and Sarjeant, Amy Alexis and Moeck, Peter and Stone-Sundberg, Jennifer and Snyder, Trevor J. and Kaminsky, Werner and Oliver, Allen G. and Stern, Charlotte L. and Dawe, Louise N. and Rychkov, Denis A. and Losev, Evgeniy A. and Boldyreva, Elena V. and Tanski, Joseph M. and Bernstein, Joel and Rabeh, Wael M. and Kantardjieff, Katherine A.},
  title = {Crystallographic education in the 21st century},
  journal = {J. Appl. Crystallogr.},
  year = {2015},
  volume = {48},
  number = {6},
  pages = {1964--1975},
  url = {http://dx.doi.org/10.1107/S1600576715016830},
  doi = {https://doi.org/10.1107/S1600576715016830}
}
Bernstein, H.J., Bollinger, J.C., Brown, I.D., Gražulis, S., Hester, J.R., McMahon, B., Spadaccini, N., Westbrook, J.D. and Westrip, S.P. Specification of the Crystallographic Information File format, version 2.0 2016 J. Appl. Crystallogr.
Vol. 49(1), pp. 277-284 
article DOI URL 
Abstract: Version 2.0 of the CIF format incorporates novel features implemented
in STAR 2.0. Among these are an expanded character repertoire, new
and more flexible forms for quoted data values, and new compound
data types. The CIF 2.0 format is compared with both CIF 1.1 and
STAR 2.0, and a formal syntax specification is provided.
BibTeX:
@article{Bernstein2016,
  author = {Bernstein, Herbert J. and Bollinger, John C. and Brown, I. David and Gražulis, Saulius and Hester, James R. and McMahon, Brian and Spadaccini, Nick and Westbrook, John D. and Westrip, Simon P.},
  title = {Specification of the Crystallographic Information File format, version 2.0},
  journal = {J. Appl. Crystallogr.},
  publisher = {International Union of Crystallography (IUCr)},
  year = {2016},
  volume = {49},
  number = {1},
  pages = {277--284},
  url = {http://dx.doi.org/10.1107/S1600576715021871},
  doi = {https://doi.org/10.1107/s1600576715021871}
}
Merkys, A., Vaitkus, A., Butkus, J., Okulič-Kazarinas, M., Kairys, V. and Gražulis, S. COD::CIF::Parser: an error-correcting CIF parser for the Perl language 2016 J. Appl. Crystallogr.
Vol. 49(1), pp. 292-301 
article DOI URL 
Abstract: A syntax-correcting CIF parser, COD::CIF::Parser, is presented
that can parse CIF 1.1 files and accurately report the position and
the nature of the discovered syntactic problems. In addition, the
parser is able to automatically fix the most common and the most
obvious syntactic deficiencies of the input files. Bindings for Perl,
C and Python programming environments are available. Based on
COD::CIF::Parser, the cod-tools package for manipulating the
CIFs in the Crystallography Open Database (COD) has been developed.
The cod-tools package has been successfully used for continuous
updates of the data in the automated COD data deposition pipeline,
and to check the validity of COD data against the IUCr data validation
guidelines. The performance, capabilities and applications of different
parsers are compared.
BibTeX:
@article{Merkys2016,
  author = {Merkys, Andrius and Vaitkus, Antanas and Butkus, Justas and Okulič-Kazarinas, Mykolas and Kairys, Visvaldas and Gražulis, Saulius},
  title = {COD::CIF::Parser: an error-correcting CIF parser for the Perl language},
  journal = {J. Appl. Crystallogr.},
  year = {2016},
  volume = {49},
  number = {1},
  pages = {292--301},
  url = {http://dx.doi.org/10.1107/S1600576715022396},
  doi = {https://doi.org/10.1107/S1600576715022396}
}
Bartolucci, C., Lamba, D., Gražulis, S., Manakova, E. and Heumann, H. Crystal structure of wild-type chaperonin GroEL (vol 354, pg 940, 2005) 2008 J. Mol. Biol.
Vol. 380(4), pp. 775 
article DOI  
BibTeX:
@article{Bartolucci2008,
  author = {Bartolucci, Cecilia and Lamba, Doriano and Gražulis, Saulius and Manakova, Elena and Heumann, Hermann},
  title = {Crystal structure of wild-type chaperonin GroEL (vol 354, pg 940, 2005)},
  journal = {J. Mol. Biol.},
  year = {2008},
  volume = {380},
  number = {4},
  pages = {775},
  doi = {https://doi.org/10.1016/j.jmb.2005.09.101}
}
Čapkauskaitė, E., Zubrienė, A., Baranauskienė, L., Tamulaitienė, G., Manakova, E., Kairys, V., Gražulis, S., Tumkevicius, S. and Matulis, D. Design of [(2-pyrimidinylthio)acetyl]benzenesulfonamides as inhibitors of human carbonic anhydrases 2012 Eur. J. Med. Chem.
Vol. 51, pp. 259-270 
article DOI  
BibTeX:
@article{Capkauskaite2012,
  author = {Čapkauskaitė, Edita and Zubrienė, Asta and Baranauskienė, Lina and Tamulaitienė, Giedrė and Manakova, Elena and Kairys, Visvaldas and Gražulis, Saulius and Tumkevicius, Sigitas and Matulis, Daumantas},
  title = {Design of [(2-pyrimidinylthio)acetyl]benzenesulfonamides as inhibitors of human carbonic anhydrases},
  journal = {Eur. J. Med. Chem.},
  year = {2012},
  volume = {51},
  pages = {259-270},
  doi = {https://doi.org/10.1016/j.ejmech.2012.02.050}
}
Čapkauskaitė, E., Zubrienė, A., Smirnov, A., Torresan, J., Kišonaitė, M., Kazokaitė, J., Gylytė, J., Michailovienė, V., Jogaite, V., Manakova, E., Gražulis, S., Tumkevicius, S. and Matulis, D. Benzenesulfonamides with pyrimidine moiety as inhibitors of human carbonic anhydrases I, II, VI, VII, XII, and XIII 2013 Bioorganic & Medicinal Chemistry
Vol. 21(22), pp. 6937-6947 
article DOI  
BibTeX:
@article{Capkauskaite2013,
  author = {Čapkauskaitė, Edita and Zubrienė, Asta and Smirnov, Alexey and Torresan, Jolanta and Kišonaitė, Miglė and Kazokaitė, Justina and Gylytė, Joana and Michailovienė, Vilma and Jogaite, Vaida and Manakova, Elena and Gražulis, Saulius and Tumkevicius, Sigitas and Matulis, Daumantas},
  title = {Benzenesulfonamides with pyrimidine moiety as inhibitors of human carbonic anhydrases I, II, VI, VII, XII, and XIII},
  journal = {Bioorganic & Medicinal Chemistry},
  year = {2013},
  volume = {21},
  number = {22},
  pages = {6937-6947},
  doi = {https://doi.org/10.1016/j.bmc.2013.09.029}
}
Dudutienė, V., Matulienė, J., Smirnov, A., Timm, D.D., Zubrienė, A., Baranauskienė, L., Morkūnaitė, V., Smirnovienė, J., Michailovienė, V., Juozapaitienė, V., Mickevičiūte, A., Kazokaitė, J., Bakšytė, S., Kasiliauskaitė, A., Jachno, J., Revuckiene, J., Kišonaitė, M., Pilipuitytė, V., Ivanauskaitė, E., Milinaviciutė, G., Smirnovas, V., Petrikaitė, V., Kairys, V., Petrauskas, V., Norvaišas, P., Lingė, D., Gibieža, P., Čapkauskaitė, E., Zakšauskas, A., Kazlauskas, E., Manakova, E., Gražulis, S., Ladbury, J.E. and Matulis, D. Discovery and characterization of novel selective inhibitors of carbonic anhydrase IX 2014 J. Med. Chem.
Vol. 57(22), pp. 9435-9446 
article DOI  
BibTeX:
@article{Dudutiene2014,
  author = {Dudutienė, Virginija and Matulienė, Jurgita and Smirnov, Alexey and Timm, David D. and Zubrienė, Asta and Baranauskienė, Lina and Morkūnaitė, Vaida and Smirnovienė, Joana and Michailovienė, Vilma and Juozapaitienė, Vaida and Mickevičiūte, Aurelija and Kazokaitė, Justina and Bakšytė, Sandra and Kasiliauskaitė, Aistė and Jachno, Jelena and Revuckiene, Jurgita and Kišonaitė, Miglė and Pilipuitytė, Vilma and Ivanauskaitė, Eglė and Milinaviciutė, Goda and Smirnovas, Vytautas and Petrikaitė, Vilma and Kairys, Visvaldas and Petrauskas, Vytautas and Norvaišas, Povilas and Lingė, Darius and Gibieža, Paulius and Čapkauskaitė, Edita and Zakšauskas, Audrius and Kazlauskas, Egidijus and Manakova, Elena and Gražulis, Saulius and Ladbury, John E. and Matulis, Daumantas},
  title = {Discovery and characterization of novel selective inhibitors of carbonic anhydrase IX},
  journal = {J. Med. Chem.},
  year = {2014},
  volume = {57},
  number = {22},
  pages = {9435-9446},
  doi = {https://doi.org/10.1021/jm501003k}
}
Dudutienė, V., Zubrienė, A., Smirnov, A., Gylytė, J., Timm, D., Manakova, E., Gražulis, S. and Matulis, D. 4-Substituted-2,3,5,6-tetrafluorobenzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, XII, and XIII 2013 Bioorganic & Medicinal Chemistry
Vol. 21(7), pp. 2093-2106 
article DOI  
BibTeX:
@article{Dudutiene2013,
  author = {Dudutienė, Virginija and Zubrienė, Asta and Smirnov, Alexey and Gylytė, Joana and Timm, David and Manakova, Elena and Gražulis, Saulius and Matulis, Daumantas},
  title = {4-Substituted-2,3,5,6-tetrafluorobenzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, XII, and XIII},
  journal = {Bioorganic & Medicinal Chemistry},
  year = {2013},
  volume = {21},
  number = {7},
  pages = {2093-2106},
  doi = {https://doi.org/10.1016/j.bmc.2013.01.008}
}
Dudutienė, V., Zubrienė, A., Smirnov, A., Timm, D.D., Smirnovienė, J., Kazokaitė, J., Michailovienė, V., Zakšauskas, A., Manakova, E., Gražulis, S. and Matulis, D. Functionalization of fluorinated benzenesulfonamides and their inhibitory properties toward carbonic anhydrases 2015 Chemmedchem
Vol. 10(4), pp. 662-687 
article DOI  
BibTeX:
@article{Dudutiene2015,
  author = {Dudutienė, Virginija and Zubrienė, Asta and Smirnov, Alexey and Timm, David D. and Smirnovienė, Joana and Kazokaitė, Justina and Michailovienė, Vilma and Zakšauskas, Audrius and Manakova, Elena and Gražulis, Saulius and Matulis, Daumantas},
  title = {Functionalization of fluorinated benzenesulfonamides and their inhibitory properties toward carbonic anhydrases},
  journal = {Chemmedchem},
  year = {2015},
  volume = {10},
  number = {4},
  pages = {662-687},
  doi = {https://doi.org/10.1002/cmdc.201402490}
}
Golovenko, D., Manakova, E., Zakrys, L., Zaremba, M., Sasnauskas, G., Gražulis, S. and Šikšnys, V. Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme 2014 Nucleic Acids Res.
Vol. 42(6), pp. 4113-4122 
article DOI  
BibTeX:
@article{Golovenko2014,
  author = {Golovenko, Dmitrij and Manakova, Elena and Zakrys, Linas and Zaremba, Mindaugas and Sasnauskas, Giedrius and Gražulis, Saulius and Šikšnys, Virginijus},
  title = {Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme},
  journal = {Nucleic Acids Res.},
  year = {2014},
  volume = {42},
  number = {6},
  pages = {4113-4122},
  doi = {https://doi.org/10.1093/nar/gkt1368}
}
Gražulis, S., Chateigner, D., Downs, R.T., Yokochi, A.F.T., Quirós, M., Lutterotti, L., Manakova, E., Butkus, J., Moeck, P. and Le Bail, A. Crystallography Open Database -- an open-access collection of crystal structures 2009 J. Appl. Crystallogr.
Vol. 42(4), pp. 726-729 
article DOI URL 
BibTeX:
@article{Grazulis2009,
  author = {Gražulis, Saulius and Chateigner, Daniel and Downs, Robert T. and Yokochi, A. F. T. and Quirós, Miguel and Lutterotti, Luca and Manakova, Elena and Butkus, Justas and Moeck, Peter and Le Bail, Armel},
  title = {Crystallography Open Database -- an open-access collection of crystal structures},
  journal = {J. Appl. Crystallogr.},
  year = {2009},
  volume = {42},
  number = {4},
  pages = {726--729},
  url = {http://dx.doi.org/10.1107/S0021889809016690},
  doi = {https://doi.org/10.1107/S0021889809016690}
}
Gražulis, S., Daškevič, A., Merkys, A., Chateigner, D., Lutterotti, L., Quirós, M., Serebryanaya, N.R., Moeck, P., Downs, R.T. and Le Bail, A. Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration 2012 Nucleic Acids Res.
Vol. 40(D1), pp. D420-D427 
article DOI URL 
Abstract: Using an open-access distribution model, the Crystallography Open
Database (COD, http://www.crystallography.net) collects all known
‘small molecule / small to medium sized unit cell’ crystal structures
and makes them available freely on the Internet. As of today, the
COD has aggregated ∼150 000 structures, offering basic search capabilities
and the possibility to download the whole database, or parts thereof
using a variety of standard open communication protocols. A newly
developed website provides capabilities for all registered users
to deposit published and so far unpublished structures as personal
communications or pre-publication depositions. Such a setup enables
extension of the COD database by many users simultaneously. This
increases the possibilities for growth of the COD database, and is
the first step towards establishing a world wide Internet-based collaborative
platform dedicated to the collection and curation of structural knowledge.
BibTeX:
@article{Grazulis2012,
  author = {Gražulis, Saulius and Daškevič, Adriana and Merkys, Andrius and Chateigner, Daniel and Lutterotti, Luca and Quirós, Miguel and Serebryanaya, Nadezhda R. and Moeck, Peter and Downs, Robert T. and Le Bail, Armel},
  title = {Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration},
  journal = {Nucleic Acids Res.},
  year = {2012},
  volume = {40},
  number = {D1},
  pages = {D420-D427},
  url = {http://nar.oxfordjournals.org/content/40/D1/D420.abstract},
  doi = {https://doi.org/10.1093/nar/gkr900}
}
Kišonaitė, M., Zubrienė, A., Čapkauskaitė, E., Smirnov, A., Smirnovienė, J., Kairys, V., Michailovienė, V., Manakova, E., Gražulis, S. and Matulis, D. Intrinsic thermodynamics and structure correlation of benzenesulfonamides with a pyrimidine moiety binding to carbonic anhydrases I, II, VII, XII, and XIII 2014 Plos One
Vol. 9(12), pp. e114106 
article DOI  
BibTeX:
@article{Kisonaite2014,
  author = {Kišonaitė, Miglė and Zubrienė, Asta and Čapkauskaitė, Edita and Smirnov, Alexey and Smirnovienė, Joana and Kairys, Visvaldas and Michailovienė, Vilma and Manakova, Elena and Gražulis, Saulius and Matulis, Daumantas},
  title = {Intrinsic thermodynamics and structure correlation of benzenesulfonamides with a pyrimidine moiety binding to carbonic anhydrases I, II, VII, XII, and XIII},
  journal = {Plos One},
  year = {2014},
  volume = {9},
  number = {12},
  pages = {e114106},
  doi = {https://doi.org/10.1371/journal.pone.0114106}
}
Manakova, E., Golovenko, D., Gražulis, S., Zaremba, M. and Šikšnys, V. Structural mechanism of cognate DNA recognition by the BfiI restriction enzyme 2012 FEBS J.
Vol. 279, pp. 446-447 
conference DOI  
BibTeX:
@conference{Manakova2012,
  author = {Manakova, E. and Golovenko, D. and Gražulis, Saulius and Zaremba, M. and Šikšnys, V.},
  title = {Structural mechanism of cognate DNA recognition by the BfiI restriction enzyme},
  journal = {FEBS J.},
  year = {2012},
  volume = {279},
  pages = {446-447},
  doi = {https://doi.org/10.1111/j.1742-4658.2010.08705.x}
}
Manakova, E., Gražulis, S., Zaremba, M., Tamulaitienė, G., Golovenko, D. and Šikšnys, V. Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease 2012 Nucleic Acids Res.
Vol. 40(14), pp. 6741-6751 
article DOI  
BibTeX:
@article{Manakova2012a,
  author = {Manakova, Elena and Gražulis, Saulius and Zaremba, Mindaugas and Tamulaitienė, Giedrė and Golovenko, Dmitrij and Šikšnys, Virginijus},
  title = {Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease},
  journal = {Nucleic Acids Res.},
  year = {2012},
  volume = {40},
  number = {14},
  pages = {6741-6751},
  doi = {https://doi.org/10.1093/nar/gks300}
}
Matulis, D., Čapkauskaitė, E., Zubrienė, A., Baranauskienė, L., Tamulaitienė, G., Manakova, E., Kairys, V., Gražulis, S. and Tumkevicius, S. Design, synthesis, binding, crystallography, and docking of [(2-pyrimidinylthio) acetyl] benzenesulfonamides as inhibitors of human carbonic anhydrases 2013 Biophys. J.
Vol. 104(2), pp. 558A-559A 
article DOI  
BibTeX:
@article{Matulis2013,
  author = {Matulis, Daumantas and Čapkauskaitė, Edita and Zubrienė, Asta and Baranauskienė, Lina and Tamulaitienė, Giedrė and Manakova, Elena and Kairys, Visvaldas and Gražulis, Saulius and Tumkevicius, Sigitas},
  title = {Design, synthesis, binding, crystallography, and docking of [(2-pyrimidinylthio) acetyl] benzenesulfonamides as inhibitors of human carbonic anhydrases},
  journal = {Biophys. J.},
  year = {2013},
  volume = {104},
  number = {2},
  pages = {558A-559A},
  doi = {https://doi.org/10.1016/j.bpj.2012.11.3095}
}
Matulis, D., Gylytė, J., Zubrienė, A., Dudutienė, V., Smirnov, A., Manakova, L. and Gražulis, S. Structure-thermodynamics correlations of fluorinated benzensulfonamides as inhibitors of human carbonic anhydrases 2014 Biophys. J.
Vol. 106(2), pp. 262A 
conference DOI  
BibTeX:
@conference{Matulis2014,
  author = {Matulis, Daumantas and Gylytė, Joana and Zubrienė, Asta and Dudutienė, Virginija and Smirnov, Alexey and Manakova, Lena and Gražulis, Saulius},
  title = {Structure-thermodynamics correlations of fluorinated benzensulfonamides as inhibitors of human carbonic anhydrases},
  journal = {Biophys. J.},
  year = {2014},
  volume = {106},
  number = {2},
  pages = {262A},
  doi = {https://doi.org/10.1016/j.bpj.2013.11.1543}
}
Rutkauskas, K., Zubrienė, A., Tumošiene, I., Kantminienė, K., Kazemekaitė, M., Smirnov, A., Kazokaitė, J., Morkūnaitė, V., Čapkauskaitė, E., Manakova, E., Gražulis, S., Beresnevičius, Z.J. and Matulis, D. 4-Amino-substituted benzenesulfonamides as inhibitors of human carbonic anhydrases 2014 Molecules
Vol. 19(11), pp. 17356-17380 
article DOI  
BibTeX:
@article{Rutkauskas2014,
  author = {Rutkauskas, Kęstutis and Zubrienė, Asta and Tumošiene, Ingrida and Kantminienė, Kristina and Kazemekaitė, Marytė and Smirnov, Alexey and Kazokaitė, Justina and Morkūnaitė, Vaida and Čapkauskaitė, Edita and Manakova, Elena and Gražulis, Saulius and Beresnevičius, Zigmuntas J. and Matulis, Daumantas},
  title = {4-Amino-substituted benzenesulfonamides as inhibitors of human carbonic anhydrases},
  journal = {Molecules},
  year = {2014},
  volume = {19},
  number = {11},
  pages = {17356-17380},
  doi = {https://doi.org/10.3390/molecules191117356}
}
Sukackaitė, R., Gražulis, S., Tamulaitis, G. and Šikšnys, V. The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine 2012 Nucleic Acids Res.
Vol. 40(15), pp. 7552-7562 
article DOI  
BibTeX:
@article{Sukackaite2012,
  author = {Sukackaitė, Rasa and Gražulis, Saulius and Tamulaitis, Gintautas and Šikšnys, Virginijus},
  title = {The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine},
  journal = {Nucleic Acids Res.},
  year = {2012},
  volume = {40},
  number = {15},
  pages = {7552-7562},
  doi = {https://doi.org/10.1093/nar/gks332}
}
Tamulaitienė, G., Šilanskas, A., Gražulis, S., Zaremba, M. and Šikšnys, V. Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII 2014 Nucleic Acids Res.
Vol. 42(22), pp. 14022-14030 
article DOI  
BibTeX:
@article{Tamulaitiene2014,
  author = {Tamulaitienė, Giedrė and Šilanskas, Arunas and Gražulis, Saulius and Zaremba, Mindaugas and Šikšnys, Virginijus},
  title = {Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII},
  journal = {Nucleic Acids Res.},
  year = {2014},
  volume = {42},
  number = {22},
  pages = {14022-14030},
  doi = {https://doi.org/10.1093/nar/gku1237}
}
Timm, D., Zubrienė, A., Gylytė, J., Dudutienė, V., Smirnov, A., Manakova, E., Gražulis, S. and Matulis, D. Thermodynamics of inhibitor binding to several recombinant carbonic anhydrases isoforms 2013 FEBS J.
Vol. 280, pp. 148 
conference DOI  
BibTeX:
@conference{Timm2013,
  author = {Timm, D. and Zubrienė, A. and Gylytė, J. and Dudutienė, V. and Smirnov, A. and Manakova, E. and Gražulis, Saulius and Matulis, D.},
  title = {Thermodynamics of inhibitor binding to several recombinant carbonic anhydrases isoforms},
  journal = {FEBS J.},
  year = {2013},
  volume = {280},
  pages = {148},
  doi = {https://doi.org/10.1111/febs.12340}
}
Zubrienė, A., Dudutienė, V., Smirnov, A., Timm, D., Gylytė, J., Manakova, E., Gražulis, S. and Matulis, D. Thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamides binding to carbonic anhydrase isozymes 2013 Eur. Biophys. J. Biophy.
Vol. 42, pp. S185 
conference URL 
BibTeX:
@conference{Zubriene2013,
  author = {Zubrienė, A. and Dudutienė, V. and Smirnov, A. and Timm, D. and Gylytė, J. and Manakova, E. and Gražulis, Saulius and Matulis, D.},
  title = {Thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamides binding to carbonic anhydrase isozymes},
  journal = {Eur. Biophys. J. Biophy.},
  year = {2013},
  volume = {42},
  pages = {S185},
  url = {https://link.springer.com/journal/249/42/1/suppl}
}
Zubrienė, A., Smirnovienė, J., Smirnov, A., Morkūnaitė, V., Michailovienė, V., Jachno, J., Juozapaitienė, V., Norvaišas, P., Manakova, E., Gražulis, S. and Matulis, D. Intrinsic thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide binding to carbonic anhydrases by isothermal titration calorimetry 2015 Biophys. Chem.
Vol. 205, pp. 51-65 
article DOI  
BibTeX:
@article{Zubriene2015,
  author = {Zubrienė, Asta and Smirnovienė, Joana and Smirnov, Alexey and Morkūnaitė, Vaida and Michailovienė, Vilma and Jachno, Jelena and Juozapaitienė, Vaida and Norvaišas, Povilas and Manakova, Elena and Gražulis, Saulius and Matulis, Daumantas},
  title = {Intrinsic thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide binding to carbonic anhydrases by isothermal titration calorimetry},
  journal = {Biophys. Chem.},
  year = {2015},
  volume = {205},
  pages = {51-65},
  doi = {https://doi.org/10.1016/j.bpc.2015.05.009}
}
Gražulis, S., Merkys, A., Vaitkus, A. and Okulič-Kazarinas, M. Computing stoichiometric molecular composition from crystal structures 2015 J. Appl. Crystallogr.
Vol. 48, pp. 85-91 
article DOI URL 
Abstract: Crystallographic investigations deliver high-accuracy information
about positions of atoms in crystal unit cells. For chemists, however,
the structure of a molecule is most often of interest. The structure
must thus be reconstructed from crystallographic files using symmetry
information and chemical properties of atoms. Most existing algorithms
faithfully reconstruct separate molecules but not the overall stoichiometry
of the complex present in a crystal. Here, an algorithm that can
reconstruct stoichiometrically correct multimolecular ensembles is
described. This algorithm uses only the crystal symmetry information
for determining molecule numbers and their stoichiometric ratios.
The algorithm can be used by chemists and crystallographers as a
standalone implementation for investigating above-molecular ensembles
or as a function implemented in graphical crystal analysis software.
The greatest envisaged benefit of the algorithm, however, is for
the users of large crystallographic and chemical databases, since
it will permit database maintainers to generate stoichiometrically
correct chemical representations of crystal structures automatically
and to match them against chemical databases, enabling multidisciplinary
searches across multiple databases.
BibTeX:
@article{Grazulis2015,
  author = {Gražulis, Saulius and Merkys, Andrius and Vaitkus, Antanas and Okulič-Kazarinas, Mykolas},
  title = {Computing stoichiometric molecular composition from crystal structures},
  journal = {J. Appl. Crystallogr.},
  year = {2015},
  volume = {48},
  pages = {85-91},
  url = {http://dx.doi.org/10.1107/S1600576714025904},
  doi = {https://doi.org/10.1107/S1600576714025904}
}
Pepponi, G., Gražulis, S. and Chateigner, D. MPOD: A Material Property Open Database linked to structural information 2012 Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. At.
Vol. 284(0), pp. 10 - 14 
article DOI URL 
BibTeX:
@article{Pepponi2012,
  author = {Giancarlo Pepponi and Saulius Gražulis and Daniel Chateigner},
  title = {MPOD: A Material Property Open Database linked to structural information},
  journal = {Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. At.},
  year = {2012},
  volume = {284},
  number = {0},
  pages = {10 - 14},
  note = {E-MRS 2011 Spring Meeting, Symposium M: X-ray techniques for materials research-from laboratory sources to free electron lasers},
  url = {http://www.sciencedirect.com/science/article/pii/S0168583X11008639},
  doi = {https://doi.org/10.1016/j.nimb.2011.08.070}
}
Baranauskienė, L., Hilvo, M., Matulienė, J., Golovenko, D., Manakova, E., Dudutienė, V., Michailovienė, V., Torresan, J., Jachno, J., Parkkila, S., Maresca, A., Supuran, C.T., Gražulis, S. and Matulis, D. Inhibition and binding studies of carbonic anhydrase isozymes I, II and IX with benzimidazo[1,2-c][1,2,3]thiadiazole-7-sulphonamides 2010 Enzyme Inhib. Med. Chem.
Vol. 25(6), pp. 863-870 
article DOI  
BibTeX:
@article{Baranauskiene2010,
  author = {Baranauskienė, L. and Hilvo, M. and Matulienė, J. and Golovenko, D. and Manakova, E. and Dudutienė, V. and Michailovienė, V. and Torresan, J. and Jachno, J. and Parkkila, S. and Maresca, A. and Supuran, C. T. and Gražulis, Saulius and Matulis, D.},
  title = {Inhibition and binding studies of carbonic anhydrase isozymes I, II and IX with benzimidazo[1,2-c][1,2,3]thiadiazole-7-sulphonamides},
  journal = {Enzyme Inhib. Med. Chem.},
  year = {2010},
  volume = {25},
  number = {6},
  pages = {863-870},
  doi = {https://doi.org/10.3109/14756360903571685}
}
Čapkauskaitė, E., Baranauskienė, L., Golovenko, D., Manakova, E., Gražulis, S., Tumkevičius, S. and Matulis, D. Indapamide-like benzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, and XIII. 2010 Bioorg. Med. Chem.
Vol. 18(21), pp. 7357-7364School: Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania. 
article DOI URL 
Abstract: A series of novel 2-chloro-5-[(1-benzimidazolyl- and 2-benzimidazolylsulfanyl)acetyl]benzene-sulfonamides
were designed and synthesized. Their binding to recombinant human
carbonic anhydrase (hCA) isozymes I, II, VII, and XIII was determined
by isothermal titration calorimetry and thermal shift assay. The
designed S-alkylated benzimidazole derivatives exhibited stronger
binding than the indapamide-like N-alkylated benzimidazoles, with
the K(d) reaching about 50-100 nM with drug-targeted hCAs VII and
XIII. The cocrystal structures of selected compounds with hCA II
were determined by X-ray crystallography, and structural features
of the binding event were revealed.
BibTeX:
@article{Capkauskaite2010,
  author = {Edita Čapkauskaitė and Lina Baranauskienė and Dmitrij Golovenko and Elena Manakova and Saulius Gražulis and Sigitas Tumkevičius and Daumantas Matulis},
  title = {Indapamide-like benzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, and XIII.},
  journal = {Bioorg. Med. Chem.},
  school = {Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania.},
  year = {2010},
  volume = {18},
  number = {21},
  pages = {7357--7364},
  url = {http://dx.doi.org/10.1016/j.bmc.2010.09.016},
  doi = {https://doi.org/10.1016/j.bmc.2010.09.016}
}
Golovenko, D., Manakova, E., Tamulaitienė, G., Gražulis, S. and Šikšnys, V. Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. 2009 Nucleic Acids Res.
Vol. 37(19), pp. 6613-6624School: Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania. 
article DOI URL 
Abstract: EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence
(W stands for A or T); however, it shows no activity on a single
recognition site. To activate cleavage it requires binding of an
additional target site as an allosteric effector. EcoRII dimer consists
of three structural units: a central catalytic core, made from two
copies of the C-terminal domain (EcoRII-C), and two N-terminal effector
DNA binding domains (EcoRII-N). Here, we report DNA-bound EcoRII-N
and EcoRII-C structures, which show that EcoRII combines two radically
different structural mechanisms to interact with the effector and
substrate DNA. The catalytic EcoRII-C dimer flips out the central
T:A base pair and makes symmetric interactions with the CC:GG half-sites.
The EcoRII-N effector domain monomer binds to the target site asymmetrically
in a single defined orientation which is determined by specific hydrogen
bonding and van der Waals interactions with the central T:A pair
in the major groove. The EcoRII-N mode of the target site recognition
is shared by the large class of higher plant transcription factors
of the B3 superfamily.
BibTeX:
@article{Golovenko2009,
  author = {Dmitrij Golovenko and Elena Manakova and Giedrė Tamulaitienė and Saulius Gražulis and Virginijus Šikšnys},
  title = {Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.},
  journal = {Nucleic Acids Res.},
  school = {Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania.},
  year = {2009},
  volume = {37},
  number = {19},
  pages = {6613--6624},
  url = {http://dx.doi.org/10.1093/nar/gkp699},
  doi = {https://doi.org/10.1093/nar/gkp699}
}
Gražulis, S., Butkus, J., Downs, R., Olozábal, M.Q. and Le Bail, A. Software for maintaining and expanding the Crystallography Open Database 2010 Acta Crystallogr. A
Vol. 66(a1), pp. s313 
article DOI  
BibTeX:
@article{Grazulis2010,
  author = {Saulius Gražulis and Justas Butkus and Robert Downs and Miguel Quirós Olozábal and Le Bail, Armel},
  title = {Software for maintaining and expanding the Crystallography Open Database},
  journal = {Acta Crystallogr. A},
  publisher = {International Union of Crystallography (IUCr)},
  year = {2010},
  volume = {66},
  number = {a1},
  pages = {s313},
  doi = {https://doi.org/10.1107/S0108767310092810}
}
Sūdžius, J., Baranauskienė, L., Golovenko, D., Matulienė, J., Michailovienė, V., Torresan, J., Jachno, J., Sukackaitė, R., Manakova, E., Gražulis, S., Tumkevičius, S. and Matulis, D. 4-[N-(substituted 4-pyrimidinyl)amino]benzenesulfonamides as inhibitors of carbonic anhydrase isozymes I, II, VII, and XIII. 2010 Bioorg. Med. Chem.
Vol. 18(21), pp. 7413-7421School: Department of Organic Chemistry, Faculty of Chemistry, Vilnius University, Naugarduko 24, LT-03225 Vilnius, Lithuania. 
article DOI URL 
Abstract: A series of 4-[N-(substituted 4-pyrimidinyl)amino]benzenesulfonamides
were designed and synthesised. Their binding potencies as inhibitors
of selected recombinant human carbonic anhydrase (hCA) isozymes I,
II, VII, and XIII were measured using isothermal titration calorimetry
and the thermal shift assay. To determine the structural features
of inhibitor binding, the crystal structures of several compounds
in complex with hCA II were determined. Several compounds exhibited
selectivity towards isozymes I, II, and XIII, and some were potent
inhibitors of hCA VII.
BibTeX:
@article{Sudzius2010,
  author = {Jurgis Sūdžius and Lina Baranauskienė and Dmitrij Golovenko and Jurgita Matulienė and Vilma Michailovienė and Jolanta Torresan and Jelena Jachno and Rasa Sukackaitė and Elena Manakova and Saulius Gražulis and Sigitas Tumkevičius and Daumantas Matulis},
  title = {4-[N-(substituted 4-pyrimidinyl)amino]benzenesulfonamides as inhibitors of carbonic anhydrase isozymes I, II, VII, and XIII.},
  journal = {Bioorg. Med. Chem.},
  school = {Department of Organic Chemistry, Faculty of Chemistry, Vilnius University, Naugarduko 24, LT-03225 Vilnius, Lithuania.},
  year = {2010},
  volume = {18},
  number = {21},
  pages = {7413--7421},
  url = {http://dx.doi.org/10.1016/j.bmc.2010.09.011},
  doi = {https://doi.org/10.1016/j.bmc.2010.09.011}
}
Bozic, D., Gražulis, S., Šikšnys, V. and Huber, R. Crystal structure of {C}itrobacter freundii\/ restriction endonuclease {Cfr}\/10I at 2.15 Å resolution. 1996 J. Mol. Biol.
Vol. 255(1), pp. 176-186School: Max-Planck-Institut für Biochemie, Planegg-Martinsried Germany. 
article DOI URL 
Abstract: The X-ray crystal structure of Citrobacter freundii restriction endonuclease
Cfr10I has been determined at a resolution of 2.15 A by multiple
isomorphous replacement methods and refined to an R-factor of 19.64%.
The structure of Cfr10I represents the first structure of a restriction
endonuclease recognizing a degenerated nucleotide sequence. Structural
comparison of Cfr10I with previously solved structures of other restriction
enzymes suggests that recognition of specific sequence occurs through
contacts in the major and the minor grooves of DNA. The arrangement
of the putative active site residues shows some striking differences
from previously described restriction endonucleases and supports
a two-metal-ion mechanism of catalysis.
BibTeX:
@article{Bozic1996,
  author = {D. Bozic and Saulius Gražulis and V. Šikšnys and R. Huber},
  title = {Crystal structure of {C}itrobacter freundii\/ restriction endonuclease {Cfr}\/10I at 2.15 Å resolution.},
  journal = {J. Mol. Biol.},
  school = {Max-Planck-Institut für Biochemie, Planegg-Martinsried Germany.},
  year = {1996},
  volume = {255},
  number = {1},
  pages = {176--186},
  url = {http://dx.doi.org/10.1006/jmbi.1996.0015},
  doi = {https://doi.org/10.1006/jmbi.1996.0015}
}
Deibert, M., Gražulis, S., Janulaitis, A., Šikšnys, V. and Huber, R. Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 Å resolution. 1999 EMBO J.
Vol. 18(21), pp. 5805-5816School: Max-Planck-Institut für Biochemie, D-82152 Planegg-Martinsried, Germany. deibert@biochem.mpg.de 
article DOI URL 
Abstract: The MunI restriction enzyme recognizes the palindromic hexanucleotide
sequence C/AATTG (the '/' indicates the cleavage site). The crystal
structure of its active site mutant D83A bound to cognate DNA has
been determined at 1.7 A resolution. Base-specific contacts between
MunI and DNA occur exclusively in the major groove. While DNA-binding
sites of most other restriction enzymes are comprised of discontinuous
sequence segments, MunI combines all residues involved in the base-specific
contacts within one short stretch (residues R115-R121) located at
the N-terminal region of the 3(10)4 helix. The outer CG base pair
of the recognition sequence is recognized solely by R115 through
hydrogen bonds made by backbone and side chain atoms to both bases.
The mechanism of recognition of the central AATT nucleotides by MunI
is similar to that of EcoRI, which recognizes the G/AATTC sequence.
The local conformation of AATT deviates from the typical B-DNA form
and is remarkably similar to EcoRI-DNA. It appears to be essential
for specific hydrogen bonding and recognition by MunI and EcoRI.
BibTeX:
@article{Deibert1999,
  author = {M. Deibert and Saulius Gražulis and A. Janulaitis and V. Šikšnys and R. Huber},
  title = {Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 Å resolution.},
  journal = {EMBO J.},
  school = {Max-Planck-Institut für Biochemie, D-82152 Planegg-Martinsried, Germany. deibert@biochem.mpg.de},
  year = {1999},
  volume = {18},
  number = {21},
  pages = {5805--5816},
  url = {http://dx.doi.org/10.1093/emboj/18.21.5805},
  doi = {https://doi.org/10.1093/emboj/18.21.5805}
}
Deibert, M., Gražulis, S., Sasnauskas, G., Šikšnys, V. and Huber, R. Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. 2000 Nat. Struct. Biol.
Vol. 7(9), pp. 792-799School: Max-Planck-Institut für Biochemie, D-82152 Planegg-Martinsried, Germany. markus.deibert@cii.de 
article DOI URL 
Abstract: The crystal structure of the NgoMIV restriction endonuclease in complex
with cleaved DNA has been determined at 1.6 A resolution. The crystallographic
asymmetric unit contains a protein tetramer and two DNA molecules
cleaved at their recognition sites. This is the first structure of
a tetrameric restriction enzyme-DNA complex. In the tetramer, two
primary dimers are arranged back to back with two oligonucleotides
bound in clefts on opposite sides of the tetramer. The DNA molecules
retain a B-type conformation and have an enclosed angle between their
helical axes of 60 degrees. Sequence-specific interactions occur
in both the major and minor grooves. Two Mg2+ ions are located close
to the cleaved phosphate at the active site of NgoMIV. Biochemical
experiments show that interactions between the recognition sites
within the tetramer greatly increase DNA cleavage efficiency.
BibTeX:
@article{Deibert2000,
  author = {M. Deibert and Saulius Gražulis and G. Sasnauskas and V. Šikšnys and R. Huber},
  title = {Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA.},
  journal = {Nat. Struct. Biol.},
  school = {Max-Planck-Institut für Biochemie, D-82152 Planegg-Martinsried, Germany. markus.deibert@cii.de},
  year = {2000},
  volume = {7},
  number = {9},
  pages = {792--799},
  url = {http://dx.doi.org/10.1038/79032},
  doi = {https://doi.org/10.1038/79032}
}
Gražulis, S., Deibert, M., Rimseliene, R., Skirgaila, R., Sasnauskas, G., Lagunavicius, A., Repin, V., Urbanke, C., Huber, R. and Šikšnys, V. Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. 2002 Nucleic Acids Res.
Vol. 30(4), pp. 876-885School: Max-Planck Institut für Biochemie, Abt. Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried (bei München), Germany. grazulis@ibt.lt 
article DOI  
Abstract: Crystal structures of Type II restriction endonucleases demonstrate
a conserved common core and active site residues but diverse structural
elements involved in DNA sequence discrimination. Comparative structural
analysis of restriction enzymes recognizing the same nucleotide sequence
might therefore contribute to our understanding of the structural
diversity of specificity determinants within restriction enzymes.
We have solved the crystal structure of the Bacillus stearothermophilus
restriction endonuclease Bse634I by the multiple isomorphous replacement
technique to 2.17 A resolution. Bse634I is an isoschisomer of the
Cfr10I restriction enzyme whose crystal structure has been reported
previously. Comparative structural analysis of the first pair of
isoschisomeric enzymes revealed conserved structural determinants
of sequence recognition and catalysis. However, conformations of
the N-terminal subdomains differed between Bse634I/Cfr10I, suggesting
a rigid body movement that might couple DNA recognition and catalysis.
Structural similarities extend to the quaternary structure level:
crystal contacts suggest that Bse634I similarly to Cfr10I is arranged
as a tetramer. Kinetic analysis reveals that Bse634I is able to interact
simultaneously with two recognition sites supporting the tetrameric
architecture of the protein. Thus, restriction enzymes Bse634I, Cfr10I
and NgoMIV, recognizing overlapping nucleotide sequences, exhibit
a conserved tetrameric architecture that is of functional importance.
BibTeX:
@article{Grazulis2002,
  author = {Saulius Gražulis and Markus Deibert and Renata Rimseliene and Remigijus Skirgaila and Giedrius Sasnauskas and Arunas Lagunavicius and Vladimir Repin and Claus Urbanke and Robert Huber and Virginijus Šikšnys},
  title = {Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.},
  journal = {Nucleic Acids Res.},
  school = {Max-Planck Institut für Biochemie, Abt. Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried (bei München), Germany. grazulis@ibt.lt},
  year = {2002},
  volume = {30},
  number = {4},
  pages = {876--885},
  doi = {https://doi.org/10.1093/nar/30.4.876}
}
Lagunavicius, A., Gražulis, S., Balčiūnaitė, E., Vainius, D. and Šikšnys, V. DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: involvement of active site carboxylate residues. 1997 Biochemistry
Vol. 36(37), pp. 11093-11099School: Institute of Biotechnology, Graiciuno 8, Vilnius 2028, Lithuania. 
article DOI URL 
Abstract: Gel shift analysis reveals [Lagunavicius, A., & Siksnys, V. (1997)
Biochemistry 36 (preceding paper in this issue)] that at pH 8.3 in
the absence of Mg2+, MunI restriction endonuclease exhibits little
DNA binding specificity, as compared with the D83A and E98A mutants
of MunI. This suggests that charged carboxylate residue(s) influence
the DNA binding specificity of MunI. In our efforts to establish
the determinants of MunI binding specificity, we investigated the
possible role of the ionic milieu, and we found that lowering pH
or elevating Ca2+ levels per se induces specific DNA recognition
by WT MunI. In contrast to the binding experiments at pH 8.3, gel
shift analysis at pH 6.5 indicated tight sequence-specific binding
of WT MunI in the absence of Mg2+, suggesting that protonation of
active site carboxylate residue(s) which manifest anomalously high
pKa value(s) control binding specificity. Interestingly, Ca2+ ion
concentrations, which did not support DNA cleavage by MunI also induced
DNA binding specificity in WT MunI at pH 8.3. To explore possible
structural changes upon DNA binding, we then used a limited proteolysis
technique. Trypsin cleavage of MunI-DNA complexes indicated that
in the presence of cognate DNA the MunI restriction endonuclease
became resistant to proteolytic cleavage, suggesting that binding
of specific DNA induced a structural change. CD measurements confirmed
this observation, suggesting minor secondary structural differences
between complexes of MunI with cognate and noncognate DNA. These
results therefore suggest that binding of MunI to its recognition
sequence triggers a conformational transition that correctly juxtaposes
active site carboxylate residues, which then chelate Mg2+ ions. In
the absence of Mg2+ ions, at pH 8.3, conditions in which carboxylate
groups would be expected to be completely ionized, electrostatic
repulsion between charged carboxylates and phosphate oxygens is enhanced
such as to interfere with specific DNA binding. Elimination of such
repulsive constraints by replacement of carboxylate residues, by
lowering pH, or by metal ion binding, then promotes MunI binding
specificity.
BibTeX:
@article{Lagunavicius1997,
  author = {A. Lagunavicius and Saulius Gražulis and E. Balčiūnaitė and D. Vainius and V. Šikšnys},
  title = {DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: involvement of active site carboxylate residues.},
  journal = {Biochemistry},
  school = {Institute of Biotechnology, Graiciuno 8, Vilnius 2028, Lithuania.},
  year = {1997},
  volume = {36},
  number = {37},
  pages = {11093--11099},
  url = {http://dx.doi.org/10.1021/bi963126a},
  doi = {https://doi.org/10.1021/bi963126a}
}
Šikšnys, V., Skirgaila, R., Sasnauskas, G., Urbanke, C., Cherny, D., Gražulis, S. and Huber, R. The Cfr10I restriction enzyme is functional as a tetramer. 1999 J. Mol. Biol.
Vol. 291(5), pp. 1105-1118School: Institute of Biotechnology, Lithuania. Siksnys@ibt.lt 
article DOI URL 
Abstract: It is thought that most of the type II restriction endonucleases interact
with DNA as homodimers. Cfr10I is a typical type II restriction enzyme
that recognises the 5'-Pu decreases CCGGPy sequence and cleaves it
as indicated by the arrow. Gel-filtration and analytical ultracentrifugation
data presented here indicate that Cfr10I is a homotetramer in isolation.
The only SfiI restriction enzyme that recognises the long interrupted
recognition sequence 5'-GGCCNNNNNGGCC has been previously reported
to operate as a tetramer however, its structure is unknown. Analysis
of Cfr10I crystals revealed that a single molecule in the asymmetric
unit is repeated by D2 symmetry to form a tetramer. To determine
whether the packing of the Cfr10I in the crystal reflects the quaternary
structure of the protein in solution, the tryptophan W220 residue
located at the putative dimer-dimer interface was mutated to alanine,
and the structural and functional consequences of the substitution
were analysed. Equilibrium sedimentation experiments revealed that,
in contrast to the wild-type Cfr10I, the W220A mutant exists in solution
predominantly as a dimer. In addition, the tetramer seems to be a
catalytically important form of Cfr10I, since the DNA cleavage activity
of the W220A mutant is < 0.1% of that of the wild-type enzyme. Further,
analysis of plasmid DNA cleavage suggests that the Cfr10I tetramer
is able to interact with two copies of the recognition sequence,
located on the same DNA molecule. Indeed, electron microscopy studies
demonstrated that two distant recognition sites are brought together
through the DNA looping induced by the simultaneous binding of the
Cfr10I tetramer to both sites. These data are consistent with the
tetramer being a functionally important form of Cfr10I.
BibTeX:
@article{Siksnys1999,
  author = {V. Šikšnys and R. Skirgaila and G. Sasnauskas and C. Urbanke and D. Cherny and Saulius Gražulis and R. Huber},
  title = {The Cfr10I restriction enzyme is functional as a tetramer.},
  journal = {J. Mol. Biol.},
  school = {Institute of Biotechnology, Lithuania. Siksnys@ibt.lt},
  year = {1999},
  volume = {291},
  number = {5},
  pages = {1105--1118},
  url = {http://dx.doi.org/10.1006/jmbi.1999.2977},
  doi = {https://doi.org/10.1006/jmbi.1999.2977}
}
Skirgaila, R., Gražulis, S., Bozic, D., Huber, R. and Šikšnys, V. Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues. 1998 J. Mol. Biol.
Vol. 279(2), pp. 473-481School: Institute of Biotechnology, Vilnius, Lithuania. 
article DOI URL 
Abstract: According to the crystal structure of Cfr10I restriction endonuclease
the acidic residues D134, E71 and E204 are clustered together and
presumably chelate metal ion(s) at the active site. Indeed, investigation
of the DNA cleavage properties of substitutional mutants of Cfr10I
D134A, E71Q, E71A and E204Q reveals that D134, E71 and E204 residues
are essential for cleavage activity, supporting their active site
function. Structural comparison indicates that the D134 residue of
Cfr10I spatially overlaps with aspartate residues D91 and D74, from
the invariant active site motifs 90PDX19EAK and 73PDX15DIK of EcoRI
and EcoRV, respectively. However, structural studies in conjunction
with mutational analyses suggest that the sequence motif 133PDX55KX13E
corresponds to the active site of Cfr10I, but differs from canonical
active site motifs of EcoRI and EcoRV. According to the crystal structure
of Cfr10I the serine S188 residue from the 188SVK sequence motif
is a spatial equivalent of the acidic residue from the (E/D)XK-part
of the active site motif, which is conserved between EcoRI and EcoRV.
Site-directed mutagenesis experiments of Cfr10I, however, revealed
that the S188 was not so important for catalysis while the E204 residue
located 2.8 A away indeed was essential for cleavage, suggesting
that the glutamate E204 rather than the S188 residue contributes
to the metal binding site in Cfr10I. In addition, model-building
studies suggest that mutual interchange of the E204 and S188 residues
should lead only to minor positional differences of the carboxylate
residues of glutamate side-chains. The double mutant S188E/E204S
was therefore prepared by site-directed mutagenesis where the active
site motif 133PDX55KX13E of Cfr10I was changed to a canonical motif
133PDX53EVK, which is similar to that of EcoRI and EcoRV. Interestingly,
the double mutant S188E/E204S of Cfr10I with redesigned active site
structure, exhibited 10% of Wt cleavage activity in a gamma DNA
cleavage assay. Thus, structure guided redesign of the catalytic/metal
binding site of Cfr10I, provides novel experimental evidence to suggest
that spatial rather than sequence conservation plays the dominant
role in the formation of restriction enzyme active sites.
BibTeX:
@article{Skirgaila1998,
  author = {R. Skirgaila and Saulius Gražulis and D. Bozic and R. Huber and V. Šikšnys},
  title = {Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues.},
  journal = {J. Mol. Biol.},
  school = {Institute of Biotechnology, Vilnius, Lithuania.},
  year = {1998},
  volume = {279},
  number = {2},
  pages = {473--481},
  url = {http://dx.doi.org/10.1006/jmbi.1998.1803},
  doi = {https://doi.org/10.1006/jmbi.1998.1803}
}
Sukackaitė, R., Gražulis, S., Bochtler, M. and Šikšnys, V. The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3 Å resolution. 2008 J. Mol. Biol.
Vol. 378(5), pp. 1084-1093School: Institute of Biotechnology, Graiciuno 8, 02241 Vilnius, Lithuania. 
article DOI URL 
Abstract: Type IIS restriction endonucleases recognize asymmetric DNA sequences
and cleave both DNA strands at fixed positions downstream of the
recognition site. The restriction endonuclease BpuJI recognizes the
asymmetric sequence 5'-CCCGT; however, it cuts at multiple sites
in the vicinity of the target sequence. BpuJI consists of two physically
separate domains, with catalytic and dimerization functions in the
C-terminal domain and DNA recognition functions in the N-terminal
domain. Here we report the crystal structure of the BpuJI recognition
domain bound to cognate DNA at 1.3-A resolution. This region folds
into two winged-helix subdomains, D1 and D2, interspaced by the DL
subdomain. The D1 and D2 subdomains of BpuJI share structural similarity
with the similar subdomains of the FokI DNA-binding domain; however,
their orientations in protein-DNA complexes are different. Recognition
of the 5'-CCCGT target sequence is achieved by BpuJI through the
major groove contacts of amino acid residues located on both the
helix-turn-helix motifs and the N-terminal arm. The role of these
interactions in DNA recognition is also corroborated by mutational
analysis.
BibTeX:
@article{Sukackaite2008,
  author = {Rasa Sukackaitė and Saulius Gražulis and Matthias Bochtler and Virginijus Šikšnys},
  title = {The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3 Å resolution.},
  journal = {J. Mol. Biol.},
  school = {Institute of Biotechnology, Graiciuno 8, 02241 Vilnius, Lithuania.},
  year = {2008},
  volume = {378},
  number = {5},
  pages = {1084--1093},
  url = {http://dx.doi.org/10.1016/j.jmb.2008.03.041},
  doi = {https://doi.org/10.1016/j.jmb.2008.03.041}
}
Tamulaitienė, G., Gražulis, S., Janulaitis, A., Janowski, R., Bujacz, G. and Jaskolski, M. Crystallization and preliminary crystallographic studies of a bifunctional restriction endonuclease Eco57I. 2004 Biochim. Biophys. Acta
Vol. 1698(2), pp. 251-254School: Institute of Biotechnology, Graiciuno 8, LT2028 Vilnius, Lithuania. eigie@ibt.lt 
article DOI URL 
Abstract: Restriction endonuclease Eco57I from Escherichia coli recognizes asymmetric
DNA sequence 5'-CTGAAG and has both restriction (DNA cleavage a short
distance away from the recognition site) and modification (methylation)
activities residing in a single polypeptide chain. Single crystals
of wild-type Eco57I ternary complexes with double-stranded DNA and
sinefungin, a stimulator of endonuclease activity, were obtained
by the vapor diffusion technique and characterized crystallographically
for different variants of the DNA component. The best data for the
complex with 25-mer DNA were collected to 4.2-A resolution at 100
K using synchrotron radiation. The crystals are orthorhombic, space
group P2(1)2(1)2, with a=164.3, b=293.0, c=71.1 A, and contain two
to four copies of the protein in the asymmetric unit.
BibTeX:
@article{Tamulaitiene2004,
  author = {Giedrė Tamulaitienė and Saulius Gražulis and Arvydas Janulaitis and Robert Janowski and Grzegorz Bujacz and Mariusz Jaskolski},
  title = {Crystallization and preliminary crystallographic studies of a bifunctional restriction endonuclease Eco57I.},
  journal = {Biochim. Biophys. Acta},
  school = {Institute of Biotechnology, Graiciuno 8, LT2028 Vilnius, Lithuania. eigie@ibt.lt},
  year = {2004},
  volume = {1698},
  number = {2},
  pages = {251--254},
  url = {http://dx.doi.org/10.1016/j.bbapap.2003.12.006},
  doi = {https://doi.org/10.1016/j.bbapap.2003.12.006}
}
Tamulaitienė, G., Jakubauskas, A., Urbanke, C., Huber, R., Gražulis, S. and Šikšnys, V. The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture. 2006 Structure
Vol. 14(9), pp. 1389-1400School: Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania. 
article DOI URL 
Abstract: Rare-cutting restriction enzymes are important tools in genome analysis.
We report here the crystal structure of SdaI restriction endonuclease,
which is specific for the 8 bp sequence CCTGCA/GG ("/" designates
the cleavage site). Unlike orthodox Type IIP enzymes, which are single
domain proteins, the SdaI monomer is composed of two structural domains.
The N domain contains a classical winged helix-turn-helix (wHTH)
DNA binding motif, while the C domain shows a typical restriction
endonuclease fold. The active site of SdaI is located within the
C domain and represents a variant of the canonical PD-(D/E)XK motif.
SdaI determinants of sequence specificity are clustered on the recognition
helix of the wHTH motif at the N domain. The modular architecture
of SdaI, wherein one domain mediates DNA binding while the other
domain is predicted to catalyze hydrolysis, distinguishes SdaI from
previously characterized restriction enzymes interacting with symmetric
recognition sequences.
BibTeX:
@article{Tamulaitiene2006,
  author = {Giedrė Tamulaitienė and Arturas Jakubauskas and Claus Urbanke and Robert Huber and Saulius Gražulis and Virginijus Šikšnys},
  title = {The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.},
  journal = {Structure},
  school = {Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania.},
  year = {2006},
  volume = {14},
  number = {9},
  pages = {1389--1400},
  url = {http://dx.doi.org/10.1016/j.str.2006.07.002},
  doi = {https://doi.org/10.1016/j.str.2006.07.002}
}
Bartolucci, C., Lamba, D., Gražulis, S., Manakova, E. and Heumann, H. Crystal structure of wild-type chaperonin GroEL. 2005 J. Mol. Biol.
Vol. 354(4), pp. 940-951School: Istituto di Cristallografia, CNR, P.O. Box 10, I-00016 Monterotondo Stazione Roma, Italy. cecilia.bartolucci@ic.cnr.it 
article DOI URL 
Abstract: The 2.9A resolution crystal structure of apo wild-type GroEL was determined
for the first time and represents the reference structure, facilitating
the study of structural and functional differences observed in GroEL
variants. Until now the crystal structure of the mutant Arg13Gly,
Ala126Val GroEL was used for this purpose. We show that, due to the
mutations as well as to the presence of a crystallographic symmetry,
the ring-ring interface was inaccurately described. Analysis of the
present structure allowed the definition of structural elements at
this interface, essential for understanding the inter-ring allosteric
signal transmission. We also show unambiguously that there is no
ATP-induced 102 degrees rotation of the apical domain helix I around
its helical axis, as previously assumed in the crystal structure
of the (GroEL-KMgATP)(14) complex, and analyze the apical domain
movements. These results enabled us to compare our structure with
other GroEL crystal structures already published, allowing us to
suggest a new route through which the allosteric signal for negative
cooperativity propagates within the molecule. The proposed mechanism,
supported by known mutagenesis data, underlines the importance of
the switching of salt bridges.
BibTeX:
@article{Bartolucci2005,
  author = {Cecilia Bartolucci and Doriano Lamba and Saulius Gražulis and Elena Manakova and Hermann Heumann},
  title = {Crystal structure of wild-type chaperonin GroEL.},
  journal = {J. Mol. Biol.},
  school = {Istituto di Cristallografia, CNR, P.O. Box 10, I-00016 Monterotondo Stazione Roma, Italy. cecilia.bartolucci@ic.cnr.it},
  year = {2005},
  volume = {354},
  number = {4},
  pages = {940--951},
  url = {http://dx.doi.org/10.1016/j.jmb.2005.09.096},
  doi = {https://doi.org/10.1016/j.jmb.2005.09.096}
}
Bochtler, M., Szczepanowski, R.H., Tamulaitis, G., Gražulis, S., Czapinska, H., Manakova, E. and Šikšnys, V. Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease. 2006 EMBO J.
Vol. 25(10), pp. 2219-2229School: International Institute of Molecular and Cell Biology, Warsaw, Poland. MBochtler@iimcb.gov.pl 
article DOI URL 
Abstract: Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG
and cleaves it before the outer C to generate 5 nt 5'-overhangs.
It has been suggested that Ecl18kI is evolutionarily related to NgoMIV,
a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt 5'-overhangs.
Here, we report the crystal structure of the Ecl18kI-DNA complex
at 1.7 A resolution and compare it with the known structure of the
NgoMIV-DNA complex. We find that Ecl18kI flips both central nucleotides
within the CCNGG sequence and buries the extruded bases in pockets
within the protein. Nucleotide flipping disrupts Watson-Crick base
pairing, induces a kink in the DNA and shifts the DNA register by
1 bp, making the distances between scissile phosphates in the Ecl18kI
and NgoMIV cocrystal structures nearly identical. Therefore, the
two enzymes can use a conserved DNA recognition module, yet recognize
different sequences, and form superimposable dimers, yet generate
different cleavage patterns. Hence, Ecl18kI is the first example
of a restriction endonuclease that flips nucleotides to achieve specificity
for its recognition site.
BibTeX:
@article{Bochtler2006,
  author = {Matthias Bochtler and Roman H. Szczepanowski and Gintautas Tamulaitis and Saulius Gražulis and Honorata Czapinska and Elena Manakova and Virginijus Šikšnys},
  title = {Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.},
  journal = {EMBO J.},
  school = {International Institute of Molecular and Cell Biology, Warsaw, Poland. MBochtler@iimcb.gov.pl},
  year = {2006},
  volume = {25},
  number = {10},
  pages = {2219--2229},
  url = {http://dx.doi.org/10.1038/sj.emboj.7601096},
  doi = {https://doi.org/10.1038/sj.emboj.7601096}
}
Gražulis, S., Manakova, E., Roessle, M., Bochtler, M., Tamulaitienė, G., Huber, R. and Šikšnys, V. Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease. 2005 Proc. Natl. Acad. Sci. USA
Vol. 102(44), pp. 15797-15802School: Laboratory of Protein-DNA Interaction, Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania. grazulis@ibt.lt 
article DOI URL 
Abstract: Among all restriction endonucleases known to date, BfiI is unique
in cleaving DNA in the absence of metal ions. BfiI represents a different
evolutionary lineage of restriction enzymes, as shown by its crystal
structure at 1.9-A resolution. The protein consists of two structural
domains. The N-terminal catalytic domain is similar to Nuc, an EDTA-resistant
nuclease from the phospholipase D superfamily. The C-terminal DNA-binding
domain of BfiI exhibits a beta-barrel-like structure very similar
to the effector DNA-binding domain of the Mg(2+)-dependent restriction
enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription
factors. BfiI presumably evolved through domain fusion of a DNA-recognition
element to a nonspecific nuclease akin to Nuc and elaborated a mechanism
to limit DNA cleavage to a single double-strand break near the specific
recognition sequence. The crystal structure suggests that the interdomain
linker may act as an autoinhibitor controlling BfiI catalytic activity
in the absence of a specific DNA sequence. A psi-blast search identified
a BfiI homologue in a Mesorhizobium sp. BNC1 bacteria strain, a plant
symbiont isolated from an EDTA-rich environment.
BibTeX:
@article{Grazulis2005,
  author = {Saulius Gražulis and Elena Manakova and Manfred Roessle and Matthias Bochtler and Giedrė Tamulaitienė and Robert Huber and Virginijus Šikšnys},
  title = {Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.},
  journal = {Proc. Natl. Acad. Sci. USA},
  school = {Laboratory of Protein-DNA Interaction, Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania. grazulis@ibt.lt},
  year = {2005},
  volume = {102},
  number = {44},
  pages = {15797--15802},
  url = {http://dx.doi.org/10.1073/pnas.0507949102},
  doi = {https://doi.org/10.1073/pnas.0507949102}
}
Neely, R.K., Daujotytė, D., Gražulis, S., Magennis, S.W., Dryden, D.T.F., Klimašauskas, S. and Jones, A.C. Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes. 2005 Nucleic Acids Res.
Vol. 33(22), pp. 6953-6960School: School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK. 
article DOI URL 
Abstract: DNA base flipping is an important mechanism in molecular enzymology,
but its study is limited by the lack of an accessible and reliable
diagnostic technique. A series of crystalline complexes of a DNA
methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent
nucleobase analogue, 2-aminopurine (AP), occupies defined positions
with respect the target flipped base, have been prepared and their
structures determined at higher than 2 A resolution. From time-resolved
fluorescence measurements of these single crystals, we have established
that the fluorescence decay function of AP shows a pronounced, characteristic
response to base flipping: the loss of the very short (approximately
100 ps) decay component and the large increase in the amplitude of
the long (approximately 10 ns) component. When AP is positioned at
sites other than the target site, this response is not seen. Most
significantly, we have shown that the same clear response is apparent
when M.HhaI complexes with DNA in solution, giving an unambiguous
signal of base flipping. Analysis of the AP fluorescence decay function
reveals conformational heterogeneity in the DNA-enzyme complexes
that cannot be discerned from the present X-ray structures.
BibTeX:
@article{Neely2005,
  author = {Robert K. Neely and Dalia Daujotytė and Saulius Gražulis and Steven W. Magennis and David T. F. Dryden and Saulius Klimašauskas and Anita C. Jones},
  title = {Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes.},
  journal = {Nucleic Acids Res.},
  school = {School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK.},
  year = {2005},
  volume = {33},
  number = {22},
  pages = {6953--6960},
  url = {http://dx.doi.org/10.1093/nar/gki995},
  doi = {https://doi.org/10.1093/nar/gki995}
}