Literature DB >> 16187365

Progress over the first decade of CASP experiments.

Andriy Kryshtafovych1, Ceslovas Venclovas, Krzysztof Fidelis, John Moult.   

Abstract

CASP has now completed a decade of monitoring the state of the art in protein structure prediction. The quality of structure models produced in the latest experiment, CASP6, has been compared with that in earlier CASPs. Significant although modest progress has again been made in the fold recognition regime, and cumulatively, progress in this area is impressive. Models of previously unknown folds again appear to have modestly improved, and several mixed alpha/beta structures have been modeled in a topologically correct manner. Progress remains hard to detect in high sequence identity comparative modeling, but server performance in this area has moved forward. 2005 Wiley-Liss, Inc.

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Year:  2005        PMID: 16187365     DOI: 10.1002/prot.20740

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


  85 in total

1.  Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase.

Authors:  Qiong Wei; Liqun Wang; Qiang Wang; Warren D Kruger; Roland L Dunbrack
Journal:  Proteins       Date:  2010-07

2.  PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences.

Authors:  K Ganesan; S Parthasarathy
Journal:  J Struct Funct Genomics       Date:  2011-12-03

3.  Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction.

Authors:  Andriy Kryshtafovych; John Moult; Sergio G Bartual; J Fernando Bazan; Helen Berman; Darren E Casteel; Evangelos Christodoulou; John K Everett; Jens Hausmann; Tatjana Heidebrecht; Tanya Hills; Raymond Hui; John F Hunt; Jayaraman Seetharaman; Andrzej Joachimiak; Michael A Kennedy; Choel Kim; Andreas Lingel; Karolina Michalska; Gaetano T Montelione; José M Otero; Anastassis Perrakis; Juan C Pizarro; Mark J van Raaij; Theresa A Ramelot; Francois Rousseau; Liang Tong; Amy K Wernimont; Jasmine Young; Torsten Schwede
Journal:  Proteins       Date:  2011-10-21

4.  An automatic method for CASP9 free modeling structure prediction assessment.

Authors:  Qian Cong; Lisa N Kinch; Jimin Pei; Shuoyong Shi; Vyacheslav N Grishin; Wenlin Li; Nick V Grishin
Journal:  Bioinformatics       Date:  2011-10-12       Impact factor: 6.937

5.  Union of geometric constraint-based simulations with molecular dynamics for protein structure prediction.

Authors:  Tyler J Glembo; S Banu Ozkan
Journal:  Biophys J       Date:  2010-03-17       Impact factor: 4.033

6.  Sub-AQUA: real-value quality assessment of protein structure models.

Authors:  Yifeng David Yang; Preston Spratt; Hao Chen; Changsoon Park; Daisuke Kihara
Journal:  Protein Eng Des Sel       Date:  2010-06-04       Impact factor: 1.650

7.  Relative packing groups in template-based structure prediction: cooperative effects of true positive constraints.

Authors:  Ryan Day; Xiaotao Qu; Rosemarie Swanson; Zach Bohannan; Robert Bliss; Jerry Tsai
Journal:  J Comput Biol       Date:  2011-01       Impact factor: 1.479

8.  Assessment of protein structure refinement in CASP9.

Authors:  Justin L MacCallum; Alberto Pérez; Michael J Schnieders; Lan Hua; Matthew P Jacobson; Ken A Dill
Journal:  Proteins       Date:  2011-08-30

9.  Computational predictions of the mutant behavior of AraC.

Authors:  Monica Berrondo; Jeffrey J Gray; Robert Schleif
Journal:  J Mol Biol       Date:  2010-03-23       Impact factor: 5.469

10.  Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels.

Authors:  Andriy Anishkin; Adina L Milac; H Robert Guy
Journal:  Proteins       Date:  2010-03
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