We are interested in residues interactions/contacts statistics for known drugs (SMALL MOLECULES ONLY, less than 50 heavy atoms).
Technically, we want to perform a structural search for every molecule in DrugBank, downloadable from
[url removed, login to view]
For every molecule from the drug bank list, we want to read the following fields:
1) drug type (approved drug, failed drug, candidate);
2) molecule type (small molecule, mixture, macromolecule);
3) unique target name (if possible);
4) all target name(s) as specified in DrugBank and/or PDB;
5) list of PDB IDs with experimental 3D structures of protein-drug complex.
For each of the drug, for each given PDB IDs from [url removed, login to view] we need:
1) info about 3D structure (year of creation, type (X-Ray or NMR), temperature, resolution);
2) whenever the protein is full or just a fragment;
3) unique protein name, so that all PDBs of exactly the same protein having the same name, and proteins from different species and/or different mutants having different names (if possible);
4) the hetgroup name (3-letter code) used for the drug in PDB file;
5) SDF file with 3D positions from PDB and correct connectivity info (including bond order and aromaticity) from DrugBank SDF; one file per each drug molecule in PDB; if the order of atoms in DrugBank SDF and in PDB is different, a file with correspondence between the two must be given;
6) general stus (all Ok; bad PDB; bad hetgroups in PDB etc.).
Using the sdf of the molecules (drugs) and the pdb files of the proteins we ask you to produces the list of all contacts of the drug and any of the residueds types from following list: lysine, tyrosine, serine, histidine, cysteine, threonine.
The results of the work should be provided as a report, the list of the contacts per drug, and the software.
In general, provide as many information from template above as possible, stopping only when absence of data or some error (for example, the molecule in DrugBank and molecule in PDB do not mach) make proceeding further impossible. On stop, give the reason for the stop.
The report must be well-structured, well-documented and machine-readable.