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• W2265106521 endingPage "2842" @default.
• W2265106521 startingPage "2836" @default.
• W2265106521 abstract "Abstract Motivation: Design of protein–protein interaction (PPI) inhibitors is a key challenge in structural bioinformatics and computer-aided drug design. Peptides, which partially mimic the interface area of one of the interacting proteins, are natural candidates to form protein–peptide complexes competing with the original PPI. The prediction of such complexes is especially challenging due to the high flexibility of peptide conformations. Results: In this article, we present PepCrawler, a new tool for deriving binding peptides from protein–protein complexes and prediction of peptide–protein complexes, by performing high-resolution docking refinement and estimation of binding affinity. By using a fast path planning approach, PepCrawler rapidly generates large amounts of flexible peptide conformations, allowing backbone and side chain flexibility. A newly introduced binding energy funnel ‘steepness score’ was applied for the evaluation of the protein–peptide complexes binding affinity. PepCrawler simulations predicted high binding affinity for native protein–peptide complexes benchmark and low affinity for low-energy decoy complexes. In three cases, where wet lab data are available, the PepCrawler predictions were consistent with the data. Comparing to other state of the art flexible peptide–protein structure prediction algorithms, our algorithm is very fast, and takes only minutes to run on a single PC. Availability: http://bioinfo3d.cs.tau.ac.il/PepCrawler/ Contact: eladdons@tau.ac.il; wolfson@tau.ac.il" @default.
• W2265106521 created "2016-06-24" @default.
• W2265106521 creator A5030975599 @default.
• W2265106521 creator A5089162570 @default.
• W2265106521 date "2011-08-31" @default.
• W2265106521 modified "2023-10-11" @default.
• W2265106521 title "PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors" @default.
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• W2265106521 doi "https://doi.org/10.1093/bioinformatics/btr498" @default.
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• W2265106521 hasPublicationYear "2011" @default.
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