Bioinformatics, residues interaction statistics for known drugs
$250-750 USD
En curso
Publicado hace alrededor de 11 años
$250-750 USD
Pagado a la entrega
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
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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 [login to view URL] 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.
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 have a PhD in structural biology and work in genomics/bioinformatics field. I am quite sure I can deliver good results.
$700 USD en 15 días
5,0 (1 comentario)
2,4
2,4
12 freelancers están ofertando un promedio de $633 USD por este trabajo
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
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 know if you need additional details from me, I´ll be happy to provide them,
Best regards,
Josef Scheiber
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 extensive bioinformatics experience - mostly in R and perl. I also have an elance account which contains some of my portfolio. I would be happy to help you with this project Thanks,
-Satwik
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 well. Will use PDBe for target data. Thanks