Generalized fragment picking in Rosetta: design, protocols and applications

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...

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Bibliographic Details
Published in:PloS one 2011-08, Vol.6 (8), p.e23294-e23294
Main Authors: Gront, Dominik, Kulp, Daniel W, Vernon, Robert M, Strauss, Charlie E M, Baker, David
Format: Article
Language:English
Subjects:
amino acid substitution
Amino acids
BASIC BIOLOGICAL SCIENCES
biochemical simulations
Bioinformatics
Biology
built structures
Computational Biology - methods
Computer simulation
Databases, Protein
Fragmentation
Fragments
Laboratories
Libraries
Mathematical models
Modelling
Models, Molecular
Modularity
NMR
Nuclear magnetic resonance
Picking
protein sequencing
protein structure
protein structure databases
protein structure prediction
Proteins
Software
structural proteins
Ubiquitin - chemistry
Workflow
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Description
Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0023294