Title |
Generalized Fragment Picking in Rosetta: Design, Protocols and Applications
|
---|---|
Published in |
PLOS ONE, August 2011
|
DOI | 10.1371/journal.pone.0023294 |
Pubmed ID | |
Authors |
Dominik Gront, Daniel W. Kulp, Robert M. Vernon, Charlie E. M. Strauss, David Baker |
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. |
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Geographical breakdown
Country | Count | As % |
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United States | 5 | 2% |
Korea, Republic of | 2 | <1% |
Germany | 2 | <1% |
Italy | 1 | <1% |
Canada | 1 | <1% |
United Kingdom | 1 | <1% |
Russia | 1 | <1% |
Serbia | 1 | <1% |
Unknown | 197 | 93% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 69 | 33% |
Researcher | 55 | 26% |
Student > Master | 18 | 9% |
Student > Bachelor | 15 | 7% |
Student > Doctoral Student | 8 | 4% |
Other | 26 | 12% |
Unknown | 20 | 9% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 68 | 32% |
Biochemistry, Genetics and Molecular Biology | 53 | 25% |
Chemistry | 32 | 15% |
Computer Science | 13 | 6% |
Physics and Astronomy | 4 | 2% |
Other | 17 | 8% |
Unknown | 24 | 11% |