CleavPredict: A platform for reasoning about matrix metalloproteinases proteolytic events

Sonu Kumar, Boris I. Ratnikov, Marat D. Kazanov, Jeffrey W. Smith, Piotr Cieplak Cieplak

Research output: Contribution to journalArticlepeer-review

34 Citations (Scopus)

Abstract

CleavPredict (http://cleavpredict.sanfordburnham.org) is a Web server for substrate cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational platform aiding the scientific community in reasoning about proteolytic events. CleavPredict offers in silico prediction of cleavage sites specific for 11 human MMPs. The prediction method employs the MMP specific position weight matrices (PWMs) derived from statistical analysis of high-throughput phage display experimental results. To augment the substrate cleavage prediction process, CleavPredict provides information about the structural features of potential cleavage sites that influence proteolysis. These include: secondary structure, disordered regions, transmembrane domains, and solvent accessibility. The server also provides information about subcellular location, co-localization, and co-expression of proteinase and potential substrates, along with experimentally determined positions of single nucleotide polymorphism (SNP), and posttranslational modification (PTM) sites in substrates. All this information will provide the user with perspectives in reasoning about proteolytic events. CleavPredict is freely accessible, and there is no login required.

Original languageEnglish
Article numbere0127877
JournalPLoS ONE
Volume10
Issue number5
DOIs
Publication statusPublished - 21 May 2015
Externally publishedYes

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