Opened: Thursday, 7 December 2023, 12:00 AM
Due: Saturday, 23 December 2023, 11:59 PM

Compare structures in PDB solved by different experimental methods.

Palyginkite PDB struktūras, išspręstas skirtingais eksperimentiniais metodais.

The goal of this assignment is to compare macromolecule structures solved by two or more different methods. Are atomic coordinates experimentally reproducible? Are they comparable between different methods? What is the accuracy of each method?

For the list of methods that you will be comparing, select a choice in [1]. Find lists of structures either using interactive PDB Web sites [2-4] or the PDB "ftp" archive [5]. Use Unix/Linux tools to locate macromolecules solved by all different methods that are listed in your choice. Document carefully your calculations: for downloads, record the download URL and time stamp (date and time); for computation of derived data and lists, record command(s) use to produce each file. Commit all your initial data, metadata (documentation of the downloads and computations) and workflows into a Subversion repository. Use time stamps on intermediate and final files. Build a Makefile that would take your downloaded files (PDB identifier lists, structure lists, structures, etc.) and automatically produce the final result files that you will use for your inferences and for the final report. Don't forge the well-known .PHONY targets (all, clean, distclean); the command sequence "make distclean; make all" MUST rerun all calculations of the derived data. Downloads can also be managed by the Makefile, BTW ;).

The experimental method lists and sequences were produced from the PDB derived data files [6,7]; they were selected in such a way that there should be at least one sequence with the structure solved by each method list. If you can not locate such sequences, please discuss this with the professor; state exact method that you use to find the sequences.

Refs.:

[1] https://emokymai.vu.lt/mod/choice/view.php?id=144335

[2] https://www.rcsb.org/

[3] https://www.ebi.ac.uk/pdbe/

[4] https://pdbj.org/

[5] https://files.wwpdb.org/pub/pdb/

[6] https://files.wwpdb.org/pub/pdb/derived_data/index/entries.idx [accessed 2023-12-05 19:54:49 +0200].

[7] https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt.gz [accessed 2023-12-05 17:05:18 +0200].