Literature DB >> 24150928

CASP10 results compared to those of previous CASP experiments.

Andriy Kryshtafovych1, Krzysztof Fidelis, John Moult.   

Abstract

We compare results of the community efforts in modeling protein structures in the tenth CASP experiment, with those in earlier CASPs particularly in CASP5, a decade ago. There is a substantial improvement in template based model accuracy as reflected in more successful modeling of regions of structure not easily derived from a single experimental structure template, most likely reflecting intensive work within the modeling community in developing methods that make use of multiple templates, as well as the increased number of experimental structures available. Deriving structural information not obvious from a template is the most demanding as well as one of the most useful tasks that modeling can perform. Thus this is gratifying progress. By contrast, overall backbone accuracy of models appears little changed in the last decade. This puzzling result is explained by two factors--increased database size in some ways makes it harder to choose the best available templates, and the increased intrinsic difficulty of CASP targets as experimental work has progressed to larger and more unusual structures. There is no detectable recent improvement in template-free modeling, but again, this may reflect the changing nature of CASP targets.
Copyright © 2013 Wiley Periodicals, Inc.

Entities:  

Keywords:  CASP; community wide experiment; protein structure prediction

Mesh:

Substances:

Year:  2013        PMID: 24150928      PMCID: PMC4180100          DOI: 10.1002/prot.24448

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


  18 in total

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Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

2.  Protein homology detection by HMM-HMM comparison.

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Journal:  Bioinformatics       Date:  2004-11-05       Impact factor: 6.937

3.  Progress over the first decade of CASP experiments.

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Authors:  Andriy Kryshtafovych; Krzysztof Fidelis; John Moult
Journal:  Proteins       Date:  2007

Review 5.  Progress and challenges in protein structure prediction.

Authors:  Yang Zhang
Journal:  Curr Opin Struct Biol       Date:  2008-04-22       Impact factor: 6.809

6.  Assessment of CASP8 structure predictions for template free targets.

Authors:  Moshe Ben-David; Orly Noivirt-Brik; Aviv Paz; Jaime Prilusky; Joel L Sussman; Yaakov Levy
Journal:  Proteins       Date:  2009

Review 7.  A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

Authors:  John Moult
Journal:  Curr Opin Struct Biol       Date:  2005-06       Impact factor: 6.809

8.  Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10.

Authors:  Andriy Kryshtafovych; John Moult; Patrick Bales; J Fernando Bazan; Marco Biasini; Alex Burgin; Chen Chen; Frank V Cochran; Timothy K Craig; Rhiju Das; Deborah Fass; Carmela Garcia-Doval; Osnat Herzberg; Donald Lorimer; Hartmut Luecke; Xiaolei Ma; Daniel C Nelson; Mark J van Raaij; Forest Rohwer; Anca Segall; Victor Seguritan; Kornelius Zeth; Torsten Schwede
Journal:  Proteins       Date:  2014-02

9.  Sampling bottlenecks in de novo protein structure prediction.

Authors:  David E Kim; Ben Blum; Philip Bradley; David Baker
Journal:  J Mol Biol       Date:  2009-07-28       Impact factor: 5.469

10.  CASP8 results in context of previous experiments.

Authors:  Andriy Kryshtafovych; Krzysztof Fidelis; John Moult
Journal:  Proteins       Date:  2009
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  43 in total

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Authors:  Jianyi Yang; Yang Zhang
Journal:  Curr Protoc Bioinformatics       Date:  2015-12-17

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Authors:  John Moult; Krzysztof Fidelis; Andriy Kryshtafovych; Torsten Schwede; Anna Tramontano
Journal:  Proteins       Date:  2017-12-15

3.  Using homology relations within a database markedly boosts protein sequence similarity search.

Authors:  Jing Tong; Ruslan I Sadreyev; Jimin Pei; Lisa N Kinch; Nick V Grishin
Journal:  Proc Natl Acad Sci U S A       Date:  2015-05-18       Impact factor: 11.205

4.  New encouraging developments in contact prediction: Assessment of the CASP11 results.

Authors:  Bohdan Monastyrskyy; Daniel D'Andrea; Krzysztof Fidelis; Anna Tramontano; Andriy Kryshtafovych
Journal:  Proteins       Date:  2015-11-17

5.  Enhanced GROMACS: toward a better numerical simulation framework.

Authors:  Hojjat Rakhshani; Effat Dehghanian; Amin Rahati
Journal:  J Mol Model       Date:  2019-11-25       Impact factor: 1.810

6.  Less is more: structures of difficult targets with minimal constraints.

Authors:  Neil R Lloyd; Deborah S Wuttke
Journal:  Structure       Date:  2014-09-02       Impact factor: 5.006

7.  Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent.

Authors:  Genki Terashi; Daisuke Kihara
Journal:  Proteins       Date:  2017-09-01

8.  Assessment of refinement of template-based models in CASP11.

Authors:  Vivek Modi; Roland L Dunbrack
Journal:  Proteins       Date:  2016-06-15

9.  WeFold: a coopetition for protein structure prediction.

Authors:  George A Khoury; Adam Liwo; Firas Khatib; Hongyi Zhou; Gaurav Chopra; Jaume Bacardit; Leandro O Bortot; Rodrigo A Faccioli; Xin Deng; Yi He; Pawel Krupa; Jilong Li; Magdalena A Mozolewska; Adam K Sieradzan; James Smadbeck; Tomasz Wirecki; Seth Cooper; Jeff Flatten; Kefan Xu; David Baker; Jianlin Cheng; Alexandre C B Delbem; Christodoulos A Floudas; Chen Keasar; Michael Levitt; Zoran Popović; Harold A Scheraga; Jeffrey Skolnick; Silvia N Crivelli
Journal:  Proteins       Date:  2014-07-08

10.  New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities.

Authors:  Clare-Louise Towse; Steven J Rysavy; Ivan M Vulovic; Valerie Daggett
Journal:  Structure       Date:  2016-01-05       Impact factor: 5.006

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