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

By John Moult, Tim J. P. Hubbard, Krzysztof Fidelis, J. Pedersen. 1999

Subfields: Evaluation & Benchmarks, Computational Biology & Bioinformatics

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Evaluation & Benchmarks

In Computational Biology & Bioinformatics

Citations in the corpus

I-TASSER server: new development for protein structure and function predictions (2015, positive): “Since CASP9, however, a new ab initio structure prediction approach, QUARK (25), has been introduced to the Zhang-Server pipeline to recognize and sort templates for the hard free modeling (FM) targets (26,27).”
TM-align: a protein structure alignment algorithm based on the TM-score (2005, neutral): “Protein structure comparisons are employed in almost all branches of contemporary structural biology, ranging from protein fold classification (1,2), protein structure modeling (3) to structure-based protein function annotation (4,5).”
High‐accuracy protein structure prediction in CASP14 (2021, background): “It can be seen therefore, that the AF2 models are close enough to the crystal structures to solve the majority of our datasets (31/32) with no modification (26), AMPLE truncation (4) or the use of individual domains (1).”
Folding membrane proteins by deep transfer learning (2017, neutral): “CMAPpro (Di Lena et al., 2012) uses a deep architecture, but its performance was worse than MetaPSICOV in CASP11 (Monastyrskyy et al., 2015).”
Pcons5: combining consensus, structural evaluation and fold recognition scores (2005, methodology): “All benchmarking results obtained in the last two years, both at CASP [21] and in LiveBench [22] indicate that consensus prediction methods are more accurate than the best of the independent fold recognition methods [10], e.”
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison (2002, methodology): “Alternative comparison metrics have been proposed, but no consensus has been established to date, as can be exemplified by the array of different approaches used in the suc- cessive CASP (critical assessment of methods of protein structure prediction, round III) meetings (Moult et al. 1999).”
MaxSub: an automated measure for the assessment of protein structure prediction quality (2000, methodology): “Mainly two types of assessment methods have been used, which, in CASP jargon, are called 'sequenceindependent' and 'sequence-dependent' (Moult et al., 1999).”
The dual role of fragments in fragment-assembly methods for de novo protein structure prediction (2011, methodology): “This factor may contribute to the small difference in median fragment quality that we observed for libraries with L [ [9,18].”
Exploiting evolutionary relationships for predicting protein structures (2003, methodology): “One such experiment, the Critical Assessment of Protein Structure Prediction (CASP) (Moult et al., 1995, 1997, 1999, 2001, 2003), clearly represents one of the most important events in the history of protein structure prediction and of the interaction between the experimental and computational…”