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Cited by 320

The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.

Modeling structurally variable regions in homologous proteins with rosetta

Rohl, Carol A., Strauss, Charlie E.M., Chivian, Dylan, Baker, David·2004·Proteins: Structure, Function, and Bioinformatics
DOI 10.1002/prot.10629
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Abstract

A major limitation of current comparative modeling methods is the accuracy with which regions that are structurally divergent from homologues of known structure can be modeled. Because structural differences between homologous proteins are responsible for variations in protein function and specificity, the ability to model these differences has important functional consequences. Although existing methods can provide reasonably accurate models of short loop regions, modeling longer structurally divergent regions is an unsolved problem. Here we describe a method based on the de novo structure prediction algorithm, Rosetta, for predicting conformations of structurally divergent regions in comparative models. Initial conformations for short segments are selected from the protein structure database, whereas longer segments are built up by using three‐ and nine‐residue fragments drawn from the database and combined by using the Rosetta algorithm. A gap closure term in the potential in combination with modified Newton's method for gradient descent minimization is used to ensure continuity of the peptide backbone. Conformations of variable regions are refined in the context of a fixed template structure using Monte Carlo minimization together with rapid repacking of side‐chains to iteratively optimize backbone torsion angles and side‐chain rotamers. For short loops, mean accuracies of 0.69, 1.45, and 3.62 Å are obtained for 4, 8, and 12 residue loops, respectively. In addition, the method can provide reasonable models of conformations of longer protein segments: predicted conformations of 3Å root‐mean‐square deviation or better were obtained for 5 of 10 examples of segments ranging from 13 to 34 residues. In combination with a sequence alignment algorithm, this method generates complete, ungapped models of protein structures, including regions both similar to and divergent from a homologous structure. This combined method was used to make predictions for 28 protein domains in the Critical Assessment of Protein Structure 4 (CASP 4) and 59 domains in CASP 5, where the method ranked highly among comparative modeling and fold recognition methods. Model accuracy in these blind predictions is dominated by alignment quality, but in the context of accurate alignments, long protein segments can be accurately modeled. Notably, the method correctly predicted the local structure of a 39‐residue insertion into a TIM barrel in CASP 5 target T0186. Proteins 2004. © 2004 Wiley‐Liss, Inc.

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Metadata

Authors
Rohl, C. A., Strauss, C. E. M., Chivian, D., & Baker, D.
Venue
Proteins: Structure, Function, and Bioinformatics
Publisher
Wiley
Published
2004-04
Volume
55
Issue
3
Pages
656-677
ISSN
  • 0887-3585 (ISSN-L)
  • 1097-0134
DOI
10.1002/prot.10629
OpenAlex
W2158307923
Cited by
320
References
45
FWCI
9.51
Type
journal article
Language
en
Open access
closed

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