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Bioinformatics. 2019 Aug 8. pii: btz623. doi: 10.1093/bioinformatics/btz623. [Epub ahead of print]

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.

Author information

1
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
2
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.

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:

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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