Assessment of ligand binding site predictions in CASP10

By Tiziano Gallo Cassarino, Lorenza Bordoli, Torsten Schwede. 2014

41 citations recorded by the source corpus.

The identification of amino acid residues in proteins involved in binding small molecule ligands is an important step for their functional characterization, as the function of a protein often depends on specific interactions with other molecules. The accuracy of computational methods aiming to predict such binding residues was evaluated within the “function prediction (prediction of binding sites, FN)” category of the critical assessment of protein structure prediction (CASP) experiment. In the last edition of the experiment (CASP10), 17 research groups participated in this category, and their predictions were evaluated on 13 prediction targets containing biologically relevant ligands. The results of this experiment indicate that several methods achieved an overall good performance, showing the usefulness of such methods in predicting ligand binding residues. As in previous years, methods based on a homology transfer approach were dominating. In comparison to CASP9, a larger fraction of the top predictors are automated servers. However, due to the small number of targets and the characteristics of the prediction format, the differences observed among the first ten methods were not statistically significant and it was also not possible to analyze differences in accuracy for different ligand types or overall structure, difficulty. To overcome these limitations and to allow for a more detailed evaluation, in future editions of CASP, methods in the FN category will no longer be evaluated on the “normal” CASP targets, but assessed continuously by CAMEO (continuous automated model evaluation) based on weekly prereleased sequences from the PDB. Proteins 2014; 82(Suppl 2):154–163. © 2013 Wiley Periodicals, Inc.

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Citations in the corpus

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences (2015, methodology): “The FunFOLD approach has performed well in recent CASP experiments (23,24).”
CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting (2022, background): “For instance, it provides a list of interaction residues with the distance threshold defined by the CASP (the sum of the van der Waals radii of the involved atoms plus a tolerance of 0.5 ˚A) (36), enabling users to obtain contact residues more conveniently.”
New prediction categories in CASP15 (2023, methodology): “32 Given the recent advances in the accuracy of protein modeling methods, 11,12 CASP organizers decided to include prediction of protein-and RNA-small molecule ligand complexes into the scope of CASP15 experiment hoping to boost development of methods in this area.”