Swimming into peptidomimetic chemical space using pepMMsMIMIC

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...

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Bibliographic Details
Published in:Nucleic acids research 2011-07, Vol.39 (suppl_2), p.W261-W269
Main Authors: Floris, Matteo, Masciocchi, Joel, Fanton, Marco, Moro, Stefano
Format: Article
Language:English
Subjects:
Biomimetic Materials - chemistry
Drug Design
Internet
Models, Molecular
Peptides - chemistry
Protein Conformation
Software
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkr287