2011
DOI: 10.1371/journal.pone.0023294
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Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

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, an… Show more

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Cited by 185 publications
(205 citation statements)
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“…The 3D model of Kivd used for rational design was built using the Rosetta Comparative Modeling protocol. 36 Fragments sets 37 and three-dimensional evolutionary constraints 38 were generated using crystal structure PDB 2VBG. A total of 1000 models were generated, and the model with the lowest energy was used as the homology model of Kivd.…”
Section: Acs Synthetic Biologymentioning
confidence: 99%
“…The 3D model of Kivd used for rational design was built using the Rosetta Comparative Modeling protocol. 36 Fragments sets 37 and three-dimensional evolutionary constraints 38 were generated using crystal structure PDB 2VBG. A total of 1000 models were generated, and the model with the lowest energy was used as the homology model of Kivd.…”
Section: Acs Synthetic Biologymentioning
confidence: 99%
“…59 Templates were identified using the HMMER3 online server, 60 and the 10 best matches based on Evalue were used as templates for molecular modeling (PDB: 2kwc, 2li5, 3vh3, 3rui, 3vxw, 2kq7, 1eo6, 4co7, 1gnu, 2r2q ). Alignments were generated using Promals3D, 61 fragments sets were generated 62 and 3D evolutionary constraints were generated using the templates. 63 RosettaCM was used to generate 1000 decoys using the threaded templates as input.…”
Section: Structure-based Model Generationmentioning
confidence: 99%
“…For example, Rosetta (Gront et al, 2011) assembles the tertiary structure from fragments consisting of up to nine residues. This sequence is long enough to span part of a b-strand, the connecting loop and a turn of a subsequent a-helix and vice versa.…”
Section: Discussionmentioning
confidence: 99%