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CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events

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

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.

Suggested Citation

  • Sonu Kumar & Boris I Ratnikov & Marat D Kazanov & Jeffrey W Smith & Piotr Cieplak, 2015. "CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-19, May.
    • Handle: RePEc:plo:pone00:0127877
    DOI: 10.1371/journal.pone.0127877
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    References listed on IDEAS

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    1. Jiangning Song & Hao Tan & Andrew J Perry & Tatsuya Akutsu & Geoffrey I Webb & James C Whisstock & Robert N Pike, 2012. "PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-23, November.
    2. Shaun R. Coughlin, 2000. "Thrombin signalling and protease-activated receptors," Nature, Nature, vol. 407(6801), pages 258-264, September.
    3. Ivo C. Lorenz & Joseph Marcotrigiano & Thomas G. Dentzer & Charles M. Rice, 2006. "Structure of the catalytic domain of the hepatitis C virus NS2-3 protease," Nature, Nature, vol. 442(7104), pages 831-835, August.
    4. Ejis, 2009. "Table of Contents," European Journal of Interdisciplinary Studies, Bucharest Economic Academy, issue 01, March.
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    1. Xuanming Guo & Jianli Cao & Jian-Piao Cai & Jiayan Wu & Jiangang Huang & Pallavi Asthana & Sheung Kin Ken Wong & Zi-Wei Ye & Susma Gurung & Yijing Zhang & Sheng Wang & Zening Wang & Xin Ge & Hiu Yee K, 2022. "Control of SARS-CoV-2 infection by MT1-MMP-mediated shedding of ACE2," Nature Communications, Nature, vol. 13(1), pages 1-17, December.

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