RT Journal Article
SR Electronic
T1 High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 174714
DO 10.1101/174714
A1 Nawsad Alam
A1 Oriel Goldstein
A1 Bing Xia
A1 Kathryn A. Porter
A1 Dima Kozakov
A1 Ora Schueler-Furman
YR 2017
UL http://biorxiv.org/content/early/2017/08/10/174714.abstract
AB Peptide-protein interactions contribute a significant fraction of the protein-protein interactome. Accurate modeling of these interactions is challenging due to the vast conformational space associated with interactions of highly flexible peptides with large receptor surfaces. To address this challenge we developed a fragment based high-resolution peptide-protein docking protocol. By streamlining the Rosetta fragment picker for accurate peptide fragment ensemble generation, the PIPER docking algorithm for exhaustive fragment-receptor rigid-body docking and Rosetta FlexPepDock for flexible full-atom refinement of PIPER docked models, we successfully addressed the challenge of accurate and efficient global peptide-protein docking at high-resolution with remarkable accuracy. Validation on a representative set of solved peptide-protein complex structures demonstrates the accuracy and robustness of our approach, and opens up the way to high-resolution modeling of many more peptide-protein interactions and to the detailed study of peptide-protein association in general. PIPER-FlexPepDock is freely available to the academic community as a server at http://piperfpd.furmanlab.cs.huji.ac.il.