Critical assessment of methods of protein structure prediction—Round VII

By John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, Burkhard Rost, Tim J. P. Hubbard, Anna Tramontano. 2007

348 citations recorded by the source corpus.

This paper is an introduction to the supplemental issue of the journal PROTEINS, dedicated to the seventh CASP experiment to assess the state of the art in protein structure prediction. The paper describes the conduct of the experiment, the categories of prediction included, and outlines the evaluation and assessment procedures. Highlights are improvements in model accuracy relative to that obtainable from knowledge of a single best template structure; convergence of the accuracy of models produced by automatic servers toward that produced by human modeling teams; the emergence of methods for predicting the quality of models; and rapidly increasing practical applications of the methods. Proteins 2007. © 2007 Wiley‐Liss, Inc.

Subfields: Conservation, History, History and Philosophy of Science, Evaluation & Benchmarks, Computational Biology & Bioinformatics

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Gaetano T. Montelione

In History and Philosophy of Science

Gaetano T. Montelione

In Evaluation & Benchmarks

In Computational Biology & Bioinformatics

Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, neutral): “[25,27,28].”
The Protein Structure Initiative: achievements and visions for the future (2012, methodology): “The PSI has also become the primary contributor of structural data that can be used for testing new methods for protein structure prediction and automated data analysis, including data used in such projects as the Critical Assessment of Structure Prediction [19,20] and the Critical Assessment of Aut”
Using inferred residue contacts to distinguish between correct and incorrect protein models (2008, background): “To what extent can inter-residue contact predictions from multiple sequence alignments, information which is orthogonal to that used in most structure prediction algorithms, be used to identify those models most similar to the native protein structure?”
An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling (2011, methodology): “However, these prior build-up strategies have not been adopted into the mainstream of structure modeling or shown to outcompete Monte Carlo or knowledge-based methods (19, 20).”
Antibody modeling assessment (2011, methodology): “Two criteria were used to assess the quality and accuracy of the models: (1) Molprobity profile31 and (2) rmsd values measured for different segments of the Fvs after overlaying various sets of backbone atoms of these or other segments of the models and the corresponding benchmark structures.”