DOI: 10.1101/507095Dec 27, 2018Paper

Decrypting protein surfaces by combining evolution, geometry and molecular docking

BioRxiv : the Preprint Server for Biology
Chloé DequekerAlessandra Carbone

Abstract

The growing body of experimental and computational data describing how proteins interact with each other has emphasized the multiplicity of protein interactions and the complexity underlying protein surface usage and deformability. In this work, we propose new concepts and methods toward deciphering such complexity. We introduce the notion of interacting region to account for the multiple usage of a protein's surface residues by several partners and for the variability of protein interfaces coming from molecular flexibility. We predict interacting patches by crossing evolutionary, physico-chemical and geometrical properties of the protein surface with information coming from complete cross-docking (CC-D) simulations. We show that our predictions match well interacting regions and that the dierent sources of information are complementary. We further propose an indicator of whether a protein has a few or many partners. Our prediction strategies are implemented in the dynJET2 algorithm and assessed on a new dataset of 262 protein on which we performed CC-D. The code and the data are available at: http://www.lcqb.upmc.fr/dynJET2/.

Related Concepts

Biological Evolution
Surface
Chemicals
Simulation
Protein-Protein Interaction
Docking -molecular Interaction

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