Assessing the binding properties of CASP14 targets and models. Issue 12 (19th August 2021)

• Record Type: Journal Article
• Authors: Egbert, Megan; Ghani, Usman; Ashizawa, Ryota; Kotelnikov, Sergei; Nguyen, Thu; Desta, Israel; Hashemi, Nasser; Padhorny, Dzmitry; Kozakov, Dima; Vajda, Sandor
• Other Names: Moult John guestEditor.; Kryshtafovych Andriy guestEditor.
• Is Part Of: Proteins. Volume 89:Issue 12(2021)
• Page Start: 1922
• Page End: 1939
• Publication Date: 2021-08-19
• Subjects: binding hot spots -- ligand docking -- protein binding site -- protein mapping -- protein–protein interaction -- quality measures -- structure prediction; Proteins -- Periodicals; Proteins -- Periodicals; 572.6
• DOI: 10.1002/prot.26209
• Languages: English
• ISSNs: 0887-3585

Abstract

Abstract: An important question is how well the models submitted to CASP retain the properties of target structures. We investigate several properties related to binding. First we explore the binding of small molecules as probes, and count the number of interactions between each residue and such probes, resulting in a binding fingerprint. The similarity between two fingerprints, one for the X‐ray structure and the other for a model, is determined by calculating their correlation coefficient. The fingerprint similarity weakly correlates with global measures of accuracy, and GDT_TS higher than 80 is a necessary but not sufficient condition for the conservation of surface binding properties. The advantage of this approach is that it can be carried out without information on potential ligands and their binding sites. The latter information was available for a few targets, and we explored whether the CASP14 models can be used to predict binding sites and to dock small ligands. Finally, we tested the ability of models to reproduce protein–protein interactions by docking both the X‐ray structures and the models to their interaction partners in complexes. The analysis showed that in CASP14 the quality of individual domain models is approaching that offered by X‐ray crystallography, and hence such models can be successfully used for the identification of binding and regulatory sites, as well as for assembling obligatory protein–protein complexes. Success of ligand docking, however, often depends on fine details of the binding interface, and thus may require accounting for conformational changes by simulation methods.