Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination

Highly coordinated water molecules are frequently an integral part of protein-protein and protein-ligand interfaces. We introduce an updated energy model that efficiently captures the energetic effects of these ordered water molecules on the surfaces of proteins. A two-stage method is developed in w...

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Published in:PLoS computational biology 2020-09, Vol.16 (9), p.e1008103-e1008103
Main Authors: Pavlovicz, Ryan E, Park, Hahnbeom, DiMaio, Frank, Singh, Mona, Wallner, Björn
Format: Article
Language:English
Subjects:
Accuracy
Amino acids
Biochemistry
Biology and Life Sciences
Computer applications
Discrimination
Docking
Energy
Engineering and Technology
Fluid dynamics
Hydrogen bonds
Interfaces
Ligands
Ligands (Biochemistry)
Monte Carlo methods
Monte Carlo simulation
Physical Sciences
Physical simulation
Physiological aspects
Protein structure
Protein-protein interactions
Proteins
Research and analysis methods
Simulation
Software
Solvents
Water
Water chemistry
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description Highly coordinated water molecules are frequently an integral part of protein-protein and protein-ligand interfaces. We introduce an updated energy model that efficiently captures the energetic effects of these ordered water molecules on the surfaces of proteins. A two-stage method is developed in which polar groups arranged in geometries suitable for water placement are first identified, then a modified Monte Carlo simulation allows highly coordinated waters to be placed on the surface of a protein while simultaneously sampling amino acid side chain orientations. This "semi-explicit" water model is implemented in Rosetta and is suitable for both structure prediction and protein design. We show that our new approach and energy model yield significant improvements in native structure recovery of protein-protein and protein-ligand docking discrimination tests.
doi_str_mv 10.1371/journal.pcbi.1008103
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subjects Accuracy
Amino acids
Biochemistry
Biology and Life Sciences
Computer applications
Discrimination
Docking
Energy
Engineering and Technology
Fluid dynamics
Hydrogen bonds
Interfaces
Ligands
Ligands (Biochemistry)
Monte Carlo methods
Monte Carlo simulation
Physical Sciences
Physical simulation
Physiological aspects
Protein structure
Protein-protein interactions
Proteins
Research and analysis methods
Simulation
Software
Solvents
Water
Water chemistry
title Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination
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