Performance of human and server prediction in CAPRI rounds 38‐45. Issue 8 (1st July 2020)

• Record Type: Journal Article
• Authors: Duan, Rui; Qiu, Liming; Xu, Xianjin; Ma, Zhiwei; Merideth, Benjamin Ryan; Shyu, Chi‐Ren; Zou, Xiaoqin
• Is Part Of: Proteins. Volume 88:Issue 8(2020)
• Page Start: 1110
• Page End: 1120
• Publication Date: 2020-07-01
• Subjects: information retrieval -- molecular docking -- protein‐peptide interactions -- protein‐protein interactions -- protein‐sugar interactions -- scoring function -- text mining; Proteins -- Periodicals; Proteins -- Periodicals; 572.6
• DOI: 10.1002/prot.25956
• Languages: English
• ISSNs: 0887-3585

Abstract

Abstract: CAPRI challenges offer a variety of blind tests for protein‐protein interaction prediction. In CAPRI Rounds 38‐45, we generated a set of putative binding modes for each target with an FFT‐based docking algorithm, and then scored and ranked these binding modes with a proprietary scoring function, ITScorePP. We have also developed a novel web server, Rebipp. The algorithm utilizes information retrieval to identify relevant biological information to significantly reduce the search space for a particular protein. In parallel, we have also constructed a GPU‐based docking server, MDockPP, for protein‐protein complex structure prediction. Here, the performance of our protocol in CAPRI rounds 38‐45 is reported, which include 16 docking and scoring targets. Among them, three targets contain multiple interfaces: Targets 124, 125, and 136 have 2, 4, and 3 interfaces, respectively. In the predictor experiments, we predicted correct binding modes for nine targets, including one high‐accuracy interface, six medium‐accuracy binding modes, and six acceptable‐accuracy binding modes. For the docking server prediction experiments, we predicted correct binding modes for eight targets, including one high‐accuracy, three medium‐accuracy, and five acceptable‐accuracy binding modes.