Useful Resources on the Web

  • DITOP: drug-induced toxicity related protein database Drug-induced toxicity related proteins (DITRPs) are proteins that mediate toxicities through their interaction with drugs or reactive metabolites. Drug-Induced Toxicity Related Protein Database (DITOP) is a comprehensive database that provides DITRPs-related information. Currently, DITOP contains 618 distinct literature-reported DITRPs, 529 drugs/ligands, and 418 distinct toxicity terms. The related toxicities include overdose toxicity, idosycratic toxicity, drug-drug interactions and genetic toxicity. 
  • Gene Design: Gene Design is aimed at researchers who want to manipulate genes, but don't want to pay for a commercial package to do so. The site's online tools allow users to alter codons in a sequence without disturbing the reading frame, insert or remove silent mutations, and perform basic analyses. These include open reading frame identification, restriction enzyme analysis/ identification, and oligonucleotide design.Web site (external)
  • Minimotif Miner (MnM): The Minimotif Miner (MnM) takes the mess of identifying short functional motifs in protein sequence out of your hands, thanks to a nifty search engine. Specifically, MnM excels at identifying "posttranslational modifications, binding to other proteins, nucleic acids, or small molecules or proteins trafficking." Use of the search algorithm couldn't be easier. Visitors enter a RefSeq number or paste in a sequence into a text box and the server does the rest, returning results in seconds. That's certainly a treat you can enjoy, and it's not even fattening. Web site (external)
  • Drug & Target Database (DrugBank): It's not difficult to find online data bases containing pharmaceutical info. A little Googling leads easily to molecular structures, lab tests, patents, side effects, and much miscellany. What's not so easy to find is a database that links drugs with data and the proteins being targeted. Fortunately, that important niche is occupied by David Wishart's DrugBank. The list of compounds in the database is impressive—over 3000 experimental compounds, greater than 1000 FDA-approved small molecules, 113 FDA-approved protein/peptides, 60+ nutraceuticals, and over 6000 protein targets (complete with sequences). Wideranging research data on each molecule is organized tidily on a "card" and much of that is cross-linked to records in related databases. If you could only go to one place to access drug data, DrugBank would be an excellent choice.Web site (external)
  • A Comprehensive Biological Pathway List: Enter Pathguide, the pathway resource list, which serves as a sort of super Rand McNally for scientists traveling across intracellular molecular freeways. With links to over 220 molecular "highways," Pathguide guides users to databases covering protein-protein interactions, metabolic pathways, signaling pathways, pathway diagrams, regulatory networks, protein-compound interactions, genetic interaction networks, and sequences of interest. Web site (external)

JOURNALS:

 

Proceedings of National Academy of Sciences of the United States of America 

 

Bioinformatics

Journal of Computational Biology

In Silico Biology

Journal of Bioinformatics and Computational Biology

Journal of Biomolecular Screening

 The Journal of Experimental Medicine