ArticleThe journal of physical chemistry. B2017
Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Article
- Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies.Molecules (Basel, Switzerland) · 2024Article
- A General Picture of Cucurbit[8]uril Host-Guest Binding: Recalibrating Bonded Interactions.Molecules (Basel, Switzerland) · 2023Article
- Early Stages of RNA-Mediated Conversion of Human Prions.The journal of physical chemistry. B · 2022Article
- Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations.Journal of computer-aided molecular design · 2021Article
- SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations.Journal of computer-aided molecular design · 2020Article
- Thermodynamics of helix formation in small peptides of varying length in vacuo, in implicit solvent, and in explicit solvent.Journal of molecular modeling · 2018Article
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3 authors.
Funding
Abstract
The physics-based potentials of side-chain-side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge-dipole or dipole-dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains. The model used in this work reproduces all features of the interacting pairs. The UNited RESidue force field with the new side-chain-side-chain interaction potentials was preliminarily tested with the N-terminal part of the B-domain of staphylococcal protein A (PDBL 1BDD ; a three-α-helix bundle) and UPF0291 protein YnzC from Bacillus subtilis (PDB: 2HEP ; an α-helical hairpin).
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