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Performance of human and server prediction in CAPRI rounds 38-45
Authors:Rui Duan  Liming Qiu  Xianjin Xu  Zhiwei Ma  Benjamin Ryan Merideth  Chi-Ren Shyu  Xiaoqin Zou
Institution:1. Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA;2. Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA

Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, USA;3. Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA

Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA;4. Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA

Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA

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.
Keywords:information retrieval  molecular docking  protein-peptide interactions  protein-protein interactions  protein-sugar interactions  scoring function  text mining
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