Electrostatic interactions in protein structure, folding, binding, and condensation

HX Zhou, X Pang - Chemical reviews, 2018‏ - ACS Publications
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …

How water's properties are encoded in its molecular structure and energies

E Brini, CJ Fennell, M Fernandez-Serra… - Chemical …, 2017‏ - ACS Publications
How are water's material properties encoded within the structure of the water molecule? This
is pertinent to understanding Earth's living systems, its materials, its geochemistry and …

FreeSolv: a database of experimental and calculated hydration free energies, with input files

DL Mobley, JP Guthrie - Journal of computer-aided molecular design, 2014‏ - Springer
This work provides a curated database of experimental and calculated hydration free
energies for small neutral molecules in water, along with molecular structures, input files …

Water models for biomolecular simulations

AV Onufriev, S Izadi - Wiley Interdisciplinary Reviews …, 2018‏ - Wiley Online Library
Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

Super-resolution in solution X-ray scattering and its applications to structural systems biology

RP Rambo, JA Tainer - Annual review of biophysics, 2013‏ - annualreviews.org
Small-angle X-ray scattering (SAXS) is a robust technique for the comprehensive structural
characterizations of biological macromolecular complexes in solution. Here, we present a …

Structural and dynamic characterizations highlight the deleterious role of SULT1A1 R213H polymorphism in substrate binding

R Dash, MC Ali, N Dash, MAK Azad… - International journal of …, 2019‏ - mdpi.com
Sulfotransferase 1A1 (SULT1A1) is responsible for catalyzing various types of endogenous
and exogenous compounds. Accumulating data indicates that the polymorphism rs9282861 …

[HTML][HTML] Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

T Sanyal, MS Shell - The Journal of chemical physics, 2016‏ - pubs.aip.org
Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG)
models for simulations at extended length and time scales but are often limited by a …

Testing inhomogeneous solvation theory in structure-based ligand discovery

TE Balius, M Fischer, RM Stein, TB Adler… - Proceedings of the …, 2017‏ - pnas.org
Binding-site water is often displaced upon ligand recognition, but is commonly neglected in
structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become …

A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration

CJ Fennell, KL Wymer, DL Mobley - The Journal of Physical …, 2014‏ - ACS Publications
We present a simple optimization strategy for incorporating experimental dielectric response
information on neat liquids in classical molecular models of alcohol. Using this strategy, we …

Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains

IS Tolokh, DE Folescu, AV Onufriev - The Journal of Physical …, 2024‏ - ACS Publications
The current practical “workhorses” of the atomistic implicit solvation─ the Poisson–
Boltzmann (PB) and generalized Born (GB) models─ face fundamental accuracy limitations …