generalized fragment picking in rosetta design, protocols and applications广义片段选择罗塞塔设计、协议和应用程序.pdfVIP

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications 1 2 3 2 4 Dominik Gront *, Daniel W. Kulp , Robert M. Vernon , Charlie E. M. Strauss , David Baker 1 Faculty of Chemistry, University of Warsaw, Warsaw, Poland, 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, United States of America, 3 Program in Molecular Structure and Function, Hospital For Sick Children, Toronto, Canada, 4 Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America Abstract The Rosetta de novo structure prediction and loop modeling protocols begin with coarse grained Monte Carlo searches in which the moves are based on short fragments extracted from a database of known structures. Here we describe a new object oriented program for picking fragments that greatly extends the functionality of the previous program (nnmake) and opens the door for new approaches to structure modeling. We provide a detailed description of the code design and architecture, highlighting its modularity, and new features such as extensibility, total control over the fragment picking workflow and scoring system customization. We demonstrate that the program provides at least as good building blocks for ab-initio structure prediction as the previous program, and provide examples of the wide range of applications that are now accessible. Citation: Gront D, Kulp DW, Vernon RM, Strauss CEM, Baker D (2011) Generalized Fragment Picking in Rosetta: Design, Protocols and Applications. PLoS ONE 6(8): e23294. doi:10.1371/journal.pone.0023294 Editor: Vladimir N. Uversky, University of South Florida College of Medicine, United States of America Received April 22,