Computational Resource for Drug Discovery explained

Computational Resources for Drug Discovery (CRDD) is an important module of the in silico module of Open Source for Drug Discovery (OSDD).[1] The CRDD web portal provides computer resources related to drug discovery, predicting inhibitors, and predicting the ADME-Tox properties of molecules on a single platform. It caters to researchers researching computer-aided drug design by providing computational resources, and hosting a discussion forum.One of the major objectives of CRDD is to promote open source software in the field of cheminformatics and pharmacoinformatics.

Features

Under CRDD, numerous resources related to computer-aided drug design have been collected and compiled. These resources are organized and presented on CRDD so users may locate resources from a single source.

Community contribution

CRDD developed a platform where the community may contribute to the process of drug discovery.

Indigenous development: software and web services

Beside collecting and compiling resources, CRDD members develop new software and web services. All services developed are free for academic use. The following are a few major tools developed at CRDD.

Development of databases

Software developed

Resources created

Web services for cheminformatics

CRDD developed an open source platform which allows users to predict inhibitors against novel M. Tuberculosis drug targets and other important properties of drug molecules like ADMET. Following are list of few servers.

Prediction and analysis of drug targets

Further reading

Notes and References

  1. Web site: Computational Resources for Drug Discovery . Computational Resources for Drug Discovery homepage.
  2. Rashid M, Singla D, Sharma A, Kumar M, Raghava GP . Hmrbase: a database of hormones and their receptors . BMC Genomics . 10 . 307 . July 2009 . 19589147 . 2720991 . 10.1186/1471-2164-10-307 . free .
  3. Singla D, Sharma A, Kaur J, Panwar B, Raghava GP . BIAdb: a curated database of benzylisoquinoline alkaloids . BMC Pharmacology . 10 . 4 . March 2010 . 20205728 . 2844369 . 10.1186/1471-2210-10-4 . free .
  4. Ansari HR, Flower DR, Raghava GP . AntigenDB: an immunoinformatics database of pathogen antigens . Nucleic Acids Research . 38 . Database issue . D847–D853 . January 2010 . 19820110 . 2808902 . 10.1093/nar/gkp830 .
  5. Aithal A, Sharma A, Joshi S, Raghava GP, Varshney GC . PolysacDB: a database of microbial polysaccharide antigens and their antibodies . PLOS ONE . 7 . 4 . e34613 . 2012-04-11 . 22509333 . 3324500 . 10.1371/journal.pone.0034613 . 2012PLoSO...734613A . Kaufmann GF . free .
  6. Kapoor P, Singh H, Gautam A, Chaudhary K, Kumar R, Raghava GP . TumorHoPe: a database of tumor homing peptides . PLOS ONE . 7 . 4 . e35187 . 2012-04-16 . 22523575 . 3327652 . 10.1371/journal.pone.0035187 . 2012PLoSO...735187K . Xue B . free .
  7. https://archive.today/20130415152313/http://nar.oxfordjournals.org/content/early/2011/12/01/nar.gkr1150.full Nucleic Acids Research, 2011
  8. Web site: Open Source Drug Discovery . 2023-09-08 . www.osdd.net.
  9. Kumar R, Chaudhary K, Gupta S, Singh H, Kumar S, Gautam A, Kapoor P, Raghava GP . 6 . CancerDR: cancer drug resistance database . Scientific Reports . 3 . 1 . 1445 . 2013-03-13 . 23486013 . 10.1038/srep01445 . 3595698 . 2013NatSR...3E1445K .
  10. Web site: Raghava . G.P.S. . MycoTB: A Software for managing Mycobacterium Tuberculosis . 2024-03-04 . crdd.osdd.net.
  11. Mishra NK, Agarwal S, Raghava GP . Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule . BMC Pharmacology . 10 . 8 . July 2010 . 20637097 . 2912882 . 10.1186/1471-2210-10-8 . free .
  12. Garg A, Tewari R, Raghava GP . KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials . BMC Bioinformatics . 11 . 125 . March 2010 . 20222969 . 2841597 . 10.1186/1471-2105-11-125 . free .
  13. Singla D, Anurag M, Dash D, Raghava GP . A web server for predicting inhibitors against bacterial target GlmU protein . BMC Pharmacology . 11 . 5 . July 2011 . 21733180 . 3146400 . 10.1186/1471-2210-11-5 . free .
  14. Kumar M, Gromiha MM, Raghava GP . SVM based prediction of RNA-binding proteins using binding residues and evolutionary information . Journal of Molecular Recognition . 24 . 2 . 303–313 . 2010 . 20677174 . 10.1002/jmr.1061 . 12677753 .
  15. Rashid, M. and Raghava, G. P. S. (2010) A simple approach for predicting protein–protein interactions. Current Protein & Peptide Science (In Press).
  16. Chauhan JS, Mishra NK, Raghava GP . Identification of ATP binding residues of a protein from its primary sequence . BMC Bioinformatics . 10 . 434 . December 2009 . 20021687 . 2803200 . 10.1186/1471-2105-10-434 . free .
  17. Mishra NK, Raghava GP . Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information . BMC Bioinformatics . 11 . Suppl 1 . S48 . January 2010 . 20122222 . 3009520 . 10.1186/1471-2105-11-S1-S48 . free .
  18. Chauhan JS, Mishra NK, Raghava GP . Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information . BMC Bioinformatics . 11 . 301 . June 2010 . 20525281 . 3098072 . 10.1186/1471-2105-11-301 . free .
  19. Ansari HR, Raghava GP . Identification of NAD interacting residues in proteins . BMC Bioinformatics . 11 . 160 . March 2010 . 20353553 . 2853471 . 10.1186/1471-2105-11-160 . free .
  20. Agarwal S, Mishra NK, Singh H, Raghava GP . Identification of mannose interacting residues using local composition . PLOS ONE . 6 . 9 . e24039 . 2011 . 21931639 . 3172211 . 10.1371/journal.pone.0024039 . free . 2011PLoSO...624039A .
  21. Panwar B, Raghava GP . Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains . BMC Genomics . 11 . 507 . September 2010 . 20860794 . 2997003 . 10.1186/1471-2164-11-507 . free .
  22. Ansari HR, Raghava GP . Identification of conformational B-cell Epitopes in an antigen from its primary sequence . Immunome Research . 6 . 6 . October 2010 . 20961417 . 2974664 . 10.1186/1745-7580-6-6 . free .
  23. Ahmed F, Raghava GP . Designing of highly effective complementary and mismatch siRNAs for silencing a gene . PLOS ONE . 6 . 8 . e23443 . 2011 . 21853133 . 3154470 . 10.1371/journal.pone.0023443 . free . 2011PLoSO...623443A .