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. 2020 Feb 1;36(3):751-757.
doi: 10.1093/bioinformatics/btz623.

Integrating Ab Initio and Template-Based Algorithms for Protein-Protein Complex Structure Prediction

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Integrating Ab Initio and Template-Based Algorithms for Protein-Protein Complex Structure Prediction

Sweta Vangaveti et al. Bioinformatics. .

Abstract

Motivation: Template-based and template-free methods have both been widely used in predicting the structures of protein-protein complexes. Template-based modeling is effective when a reliable template is available, while template-free methods are required for predicting the binding modes or interfaces that have not been previously observed. Our goal is to combine the two methods to improve computational protein-protein complex structure prediction.

Results: Here, we present a method to identify and combine high-confidence predictions of a template-based method (SPRING) with a template-free method (ZDOCK). Cross-validated using the protein-protein docking benchmark version 5.0, our method (ZING) achieved a success rate of 68.2%, outperforming SPRING and ZDOCK, with success rates of 52.1% and 35.9% respectively, when the top 10 predictions were considered per test case. In conclusion, a statistics-based method that evaluates and integrates predictions from template-based and template-free methods is more successful than either method independently.

Availability and implementation: ZING is available for download as a Github repository (https://github.com/weng-lab/ZING.git).

Supplementary information: Supplementary data are available at Bioinformatics online.

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