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Nucleic Acids Res. 2011 Jul;39(Web Server issue):W261-9. doi: 10.1093/nar/gkr287. Epub 2011 May 27.

Swimming into peptidomimetic chemical space using pepMMsMIMIC.

Author information

1
CRS4-Bioinformatics Laboratory, Parco Sardegna Ricerche, Pula (CA) 09010, Italy.

Abstract

pepMMsMIMIC is a novel web-oriented peptidomimetic compound virtual screening tool based on a multi-conformers three-dimensional (3D)-similarity search strategy. Key to the development of pepMMsMIMIC has been the creation of a library of 17 million conformers calculated from 3.9 million commercially available chemicals collected in the MMsINC® database. Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-protein recognition of this natural peptide using both pharmacophore and shape similarity techniques. We hope that the accessibility of pepMMsMIMIC (freely available at http://mms.dsfarm.unipd.it/pepMMsMIMIC) will encourage medicinal chemists to de-peptidize protein-protein recognition processes of biological interest, thus increasing the potential of in silico peptidomimetic compound screening of known small molecules to expedite drug development.

PMID:
21622954
PMCID:
PMC3125738
DOI:
10.1093/nar/gkr287
[Indexed for MEDLINE]
Free PMC Article

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