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 …

Advances in docking

VB Sulimov, DC Kutov… - Current medicinal …, 2019 - ingentaconnect.com
Background: Design of small molecules which are able to bind to the protein responsible for
a disease is the key step of the entire process of the new medicine discovery. Atomistic …

Quantitative predictions from molecular simulations using explicit or implicit interactions

D Van der Spoel, J Zhang… - Wiley Interdisciplinary …, 2022 - Wiley Online Library
Equilibrium simulations of molecular systems allow to extract many physicochemical
properties. Given an “accurate enough” model, a “large enough” simulation system and …

PocketOptimizer 2.0: A modular framework for computer‐aided ligand‐binding design

J Noske, JP Kynast, D Lemm, S Schmidt… - Protein …, 2023 - Wiley Online Library
The ability to design customized proteins to perform specific tasks is of great interest. We are
particularly interested in the design of sensitive and specific small molecule ligand‐binding …

Design of molecularly imprinted polymers (MIP) using computational methods: A review of strategies and approaches

E Mohsenzadeh, V Ratautaite, E Brazys… - Wiley …, 2024 - Wiley Online Library
This paper focuses on the computationally assisted design of molecularly imprinted
polymers (MIP), emphasizing the selected strategies and chosen methods of approach. In …

Accuracy comparison of generalized Born models in the calculation of electrostatic binding free energies

S Izadi, RC Harris, MO Fenley… - Journal of chemical …, 2018 - ACS Publications
The need for accurate yet efficient representation of the aqueous environment in
biomolecular modeling has led to the development of a variety of generalized Born (GB) …

Multidimensional global optimization and robustness analysis in the context of protein–ligand binding

N Forouzesh, A Mukhopadhyay… - Journal of chemical …, 2020 - ACS Publications
Accuracy of protein–ligand binding free energy calculations utilizing implicit solvent models
is critically affected by parameters of the underlying dielectric boundary, specifically, the …

[HTML][HTML] Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms

AV Sulimov, DA Zheltkov, IV Oferkin, DC Kutov… - Computational and …, 2017 - Elsevier
We present the novel docking algorithm based on the Tensor Train decomposition and the
TT-Cross global optimization. The algorithm is applied to the docking problem with flexible …

How well do implicit solvation models represent intermolecular binding energies in organic-inorganic solutions?

BA Sorenson, SS Hong, HC Herbol, P Clancy - Computational Materials …, 2019 - Elsevier
Computational methods, including density functional theory, are proving to be powerful
approaches to tame the otherwise overwhelming selection of optimal species and …

[HTML][HTML] A simple PB/LIE free energy function accurately predicts the peptide binding specificity of the Tiam1 PDZ domain

N Panel, YJ Sun, EJ Fuentes… - Frontiers in molecular …, 2017 - frontiersin.org
PDZ domains generally bind short amino acid sequences at the C-terminus of target
proteins, and short peptides can be used as inhibitors or model ligands. Here, we used …