Native fold and docking pose discrimination by the same residue‐based scoring function. Issue 4 (5th February 2015)

• Record Type: Journal Article
• Authors: Sarti, Edoardo; Granata, Daniele; Seno, Flavio; Trovato, Antonio; Laio, Alessandro
• Is Part Of: Proteins. Volume 83:Issue 4(2015)
• Page Start: 621
• Page End: 630
• Publication Date: 2015-02-05
• Subjects: protein‐protein interaction -- knowledge based potentials -- structure prediction -- molecular recognition -- quality assessment; Proteins -- Periodicals; Proteins -- Periodicals; 572.6
• DOI: 10.1002/prot.24764
• Languages: English
• ISSNs: 0887-3585

Abstract

ABSTRACT: Structure prediction and quality assessment are crucial steps in modeling native protein conformations. Statistical potentials are widely used in related algorithms, with different parametrizations typically developed for different contexts such as folding protein monomers or docking protein complexes. Here, we describe BACH‐SixthSense, a single residue‐based statistical potential that can be successfully employed in both contexts. BACH‐SixthSense shares the same approach as BACH, a knowledge‐based potential originally developed to score monomeric protein structures. A term that penalizes steric clashes as well as the distinction between polar and apolar sidechain‐sidechain contacts are crucial novel features of BACH‐SixthSense. The performance of BACH‐SixthSense in discriminating correctly the native structure among a competing set of decoys is significantly higher than other state‐of‐the‐art scoring functions, that were specifically trained for a single context, for both monomeric proteins (QMEAN, Rosetta, RF_CB_SRS_OD, benchmarked on CASP targets) and protein dimers (IRAD, Rosetta, PIE*PISA, HADDOCK, FireDock, benchmarked on 14 CAPRI targets). The performance of BACH‐SixthSense in recognizing near‐native docking poses within CAPRI decoy sets is good as well. Proteins 2015; 83:621–630. © 2015 Wiley Periodicals, Inc.