Critical assessment of methods of protein structure prediction (CASP): Round IV

By John Moult, Krzysztof Fidelis, Adam T. Zemla, Tim J. P. Hubbard. 2001

134 citations recorded by the source corpus.

Subfields: Molecular Biology, Evaluation & Benchmarks, Computational Biology & Bioinformatics

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Citations in the corpus

Critical Assessment of Methods of Protein Structure Prediction (CASP) – Progress and New directions in Round XI (2016, background): “(5) Methods for estimating the accuracy of models have advanced to the point where they are of considerable practical use.”
Ab initio protein structure prediction. (2002, methodology): “Advances in homology modeling and threading have been recently reviewed [5]; we will concentrate here on the recent progress in ab initio protein folding methods [6].”
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models (2006, methodology): “The first rule is also known as the 'EHL' mapping [34,35], the second rule is the one used in PSIPRED [1] and earlier outlined by Rost and Sander [36], while, finally, the third rule is the common 'CK' mapping, which is the one used in BSPSS and other methods [17,37,38].”
FragQA: predicting local fragment quality of a sequence-structure alignment. (2007, unknown): “The biennial CASP (Critical Assessment of Structure Prediction) [12] [13] [14] [15] events have demonstrated that the three-dimensional structures of many new target pro*To whom correspondence should be addressed teins can be predicted at a reasonable resolution, although in most cases, the predicte”
Protein-protein docking: from interaction to interactome. (2014, unknown): “Currently, with the rapid growth of PDB, the template-based modeling of individual proteins is a dominant approach to the prediction of protein structures (45).”
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge (2014, methodology): “Successful competitions have accelerated progress in protein folding, including the MATLAB Protein Folding Contest [15] and the International Protein Folding Competition (CASP) [16], gene identification, such as EGASP [17], and in silico tools for predicting variant pathogenicity such as the CAGI ex”
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models (2004, methodology): “Manual assessment of prediction methods, e.g. during the biannual CASP experiments (8), is a good means to evaluate new algorithmic developments based on a small number of examples.”
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. (2003, methodology): “18 In particular, the Rosetta program developed at the University of Washington is now able to construct crude ( , 5 A˚) models of many short (less than 150 amino acid residues) protein sequences.”
Can correct protein models be identified? (2003, methodology): “This is similar to the GDT_TS score used in CASP (Moult et al. 2001).”