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Literature DB >> 16187354

Free modeling with Rosetta in CASP6.

Philip Bradley¹, Lars Malmström, Bin Qian, Jack Schonbrun, Dylan Chivian, David E Kim, Jens Meiler, Kira M S Misura, David Baker.

Abstract

We describe Rosetta predictions in the Sixth Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP), focusing on the free modeling category. Methods developed since CASP5 are described, and their application to selected targets is discussed. Highlights include improved performance on larger proteins (100-200 residues) and the prediction of a 70-residue alpha-beta protein to near-atomic resolution. 2005 Wiley-Liss, Inc.

Entities: Gene

Mesh：

Year: 2005 PMID： 16187354 DOI： 10.1002/prot.20729

Source DB: PubMed Journal: Proteins ISSN： 0887-3585

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Cited

66 in total

1. Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking.

Authors: Mariah R Baker; Ian Rees; Steven J Ludtke; Wah Chiu; Matthew L Baker
Journal: Structure Date: 2012-03-07 Impact factor: 5.006

2. Molecular engineering of RANTES peptide mimetics with potent anti-HIV-1 activity.

Authors: Paolo Lusso; Luca Vangelista; Raffaello Cimbro; Massimiliano Secchi; Francesca Sironi; Renato Longhi; Marina Faiella; Ornella Maglio; Vincenzo Pavone
Journal: FASEB J Date: 2011-01-03 Impact factor: 5.191

3. Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination.

Authors: Kelli Kazmier; Nathan S Alexander; Jens Meiler; Hassane S McHaourab
Journal: J Struct Biol Date: 2010-11-11 Impact factor: 2.867

4. Multipass membrane protein structure prediction using Rosetta.

Authors: Vladimir Yarov-Yarovoy; Jack Schonbrun; David Baker
Journal: Proteins Date: 2006-03-01

5. Role of electrostatic interactions in amyloid beta-protein (A beta) oligomer formation: a discrete molecular dynamics study.

Authors: Sijung Yun; B Urbanc; L Cruz; G Bitan; D B Teplow; H E Stanley
Journal: Biophys J Date: 2007-02-16 Impact factor: 4.033

Free modeling with Rosetta in CASP6.

1. Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking.

2. Molecular engineering of RANTES peptide mimetics with potent anti-HIV-1 activity.

3. Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination.

4. Multipass membrane protein structure prediction using Rosetta.

5. Role of electrostatic interactions in amyloid beta-protein (A beta) oligomer formation: a discrete molecular dynamics study.

6. Folding pathway of the b1 domain of protein G explored by multiscale modeling.

7. Characterization of protein-folding pathways by reduced-space modeling.

8. De novo high-resolution protein structure determination from sparse spin-labeling EPR data.

9. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.

10. Solvent accessible surface area approximations for rapid and accurate protein structure prediction.