Bioinformatics, residues interaction statistics for known drugs



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.

Skills: Biology, Biotechnology, Scientific Research

See more: types of data structures in c, types of data structures, types of data structure, types data structures, type of data structures, two types of data structures, search structures, search data structures, list of data structures, list in data structures, list data structures, letter bad, different types of data structures in c, different types of data structures, different types of data structure, different types data structure, different type of data structure, different data structures, data structures types, data structures list, data structures example, bank positions, bank-creation, bad letter, about data structures in c

Project ID: #4343934

Awarded to:


Hi This project requires varied kind expertise which involves programming, thorough knowledge of structural biology and databases like PDB and drugbank as well as ability to summarize the data in professional way. I More

$700 USD in 15 days
(1 Review)

12 freelancers are bidding on average $633 for this job


sir, i am the best candidate for this job.. please check PM for details..thanks

$400 USD in 7 days
(6 Reviews)

Hi! I am a doctor and am quite interested in your project. I can do it perfectly! Thanks!

$750 USD in 20 days
(1 Review)

Hi Peter, I wrote a little script on Python and believe I will be able to do the job. The first part of the "Small molecules" Drugbank list would be the 1st milestone. Will scan KEGG and PubChem for the drug data as we More

$750 USD in 14 days
(0 Reviews)

hi i am interested in this project. i have completed M.Sc. bioinformatics.

$350 USD in 20 days
(0 Reviews)

hi i am bioinformatician, and i am interested in this project.

$300 USD in 15 days
(0 Reviews)

Biotech engineer with microbiology graduation by Catholic University.

$700 USD in 5 days
(0 Reviews)

I hold a masters degree in Computational biology and Bioinformatics, and I have a bachelors degree in Biotechnology. I have more than four years of experience doing bioinformatics. I am an expert in Python, and have ex More

$750 USD in 10 days
(0 Reviews)

Hi, I am very capable of doing this project. I am do Bayesian engineering using WinBugs. Please see my Please also see by blogs, & More

$750 USD in 2 days
(0 Reviews)

Dear Sir, I´m a PhD in Bioinformatics with lots of experience dealing with the datatypes you mention and need for your analysis. Consequently I´m sure I can deliver exactly what you need. Please let me kn More

$1300 USD in 5 days
(0 Reviews)

Hello, I am experienced Bioinformatician and a Bio IT professional and I would like to offer my candidature against your requirement. Waiting eagerly for a positive and a prompt reply. Rajdeep

$300 USD in 7 days
(0 Reviews)

Dear sir, I am ready to start your job right now. Hope to hear you soon. Thanks

$550 USD in 15 days
(0 Reviews)