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Nature Communications (2)
Nature Methods (1)

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Accurate determination of solvation free energies of neutral organic compounds from first principles

Theoretical estimations of solvation free energy by continuum solvation models are generally not accurate. Here the authors report a polarizable force field fitted entirely to first-principles calculations for the estimation of free energy of solvation of arbitrary molecules.

Leonid Pereyaslavets
Ganesh Kamath
Boris Fain
ResearchOpen Access20 Jan 2022
Nature Communications

Volume: 13, P: 1-7
CHARMM36m: an improved force field for folded and intrinsically disordered proteins

An all-atom protein force field, CHARMM36m, offers improved accuracy for simulating intrinsically disordered peptides and proteins.

Jing Huang
Sarah Rauscher
Alexander D MacKerell Jr
Research07 Nov 2016
Nature Methods

Volume: 14, P: 71-73
Reduced efficacy of a Src kinase inhibitor in crowded protein solution

The intracellular compartment is a crowded environment. Here, the authors use molecular dynamics (MD) simulations to assess inhibitor binding to c-Src kinase and show how ligand binding pathways differ in crowded and dilute protein solutions, highlighting the role of c-Src Tyr82 sidechain.

Kento Kasahara
Suyong Re
Yuji Sugita
ResearchOpen Access02 Jul 2021
Nature Communications

Volume: 12, P: 1-8