How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking.

ABSTRACT: Comparative docking is based on experimentally determined structures of protein-protein complexes (templates), following the paradigm that proteins with similar sequences and/or structures form similar complexes. Modeling utilizing structure similarity of target monomers to template complexes significantly expands structural coverage of the interactome. Template-based docking by structure alignment can be performed for the entire structures or by aligning targets to the bound interfaces of the experimentally determined complexes. Systematic benchmarking of docking protocols based on full and interface structure alignment showed that both protocols perform similarly, with top 1 docking success rate 26%. However, in terms of the models' quality, the interface-based docking performed marginal

SUBMITTER: Chakravarty D 

PROVIDER: S-EPMC7375009 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature