Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.

ABSTRACT: Ab initio protein-protein docking algorithms often rely on experimental data to identify the most likely complex structure. We integrated protein-protein docking with the experimental data of chemical cross-linking followed by mass spectrometry. We tested our approach using 19 cases that resulted from an exhaustive search of the Protein Data Bank for protein complexes with cross-links identified in our experiments. We implemented cross-links as constraints based on Euclidean distance or void-volume distance. For most test cases, the rank of the top-scoring near-native prediction was improved by at least twofold compared with docking without the cross-link information, and the success rate for the top 5 predictions nearly tripled. Our results demonstrate the delicate balance between retaini

SUBMITTER: Vreven T 

PROVIDER: S-EPMC6084434 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature