Renzhi Cao1, Badri Adhikari2, Debswapna Bhattacharya3, Miao Sun4, Jie Hou2, Jianlin Cheng2,5. 1. Department of Computer Science, Pacific Lutheran University, WA 98447, USA. 2. Department of Computer Science, University of Missouri, Columbia, MO 65211, USA. 3. Department of Electrical Engineering and Computer Science, Wichita State University, Wichita, KS 67260-0083, USA. 4. Department of Electrical and Computer Engineering. 5. Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
Abstract
Motivation: Protein model quality assessment (QA) plays a very important role in protein structure prediction. It can be divided into two groups of methods: single model and consensus QA method. The consensus QA methods may fail when there is a large portion of low quality models in the model pool. Results: In this paper, we develop a novel single-model quality assessment method QAcon utilizing structural features, physicochemical properties, and residue contact predictions. We apply residue-residue contact information predicted by two protein contact prediction methods PSICOV and DNcon to generate a new score as feature for quality assessment. This novel feature and other 11 features are used as input to train a two-layer neural network on CASP9 datasets to predict the quality of a single protein model. We blindly benchmarked our method QAcon on CASP11 dataset as the MULTICOM-CLUSTER server. Based on the evaluation, our method is ranked as one of the top single model QA methods. The good performance of the features based on contact prediction illustrates the value of using contact information in protein quality assessment. Availability and Implementation: The web server and the source code of QAcon are freely available at: http://cactus.rnet.missouri.edu/QAcon. Contact: chengji@missouri.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: Protein model quality assessment (QA) plays a very important role in protein structure prediction. It can be divided into two groups of methods: single model and consensus QA method. The consensus QA methods may fail when there is a large portion of low quality models in the model pool. Results: In this paper, we develop a novel single-model quality assessment method QAcon utilizing structural features, physicochemical properties, and residue contact predictions. We apply residue-residue contact information predicted by two protein contact prediction methods PSICOV and DNcon to generate a new score as feature for quality assessment. This novel feature and other 11 features are used as input to train a two-layer neural network on CASP9 datasets to predict the quality of a single protein model. We blindly benchmarked our method QAcon on CASP11 dataset as the MULTICOM-CLUSTER server. Based on the evaluation, our method is ranked as one of the top single model QA methods. The good performance of the features based on contact prediction illustrates the value of using contact information in protein quality assessment. Availability and Implementation: The web server and the source code of QAcon are freely available at: http://cactus.rnet.missouri.edu/QAcon. Contact: chengji@missouri.edu. Supplementary information: Supplementary data are available at Bioinformatics online.