The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy
We report the results of the SAMPL9 host–guest blind challenge for predicting binding free
energies. The challenge focused on macrocycles from pillar [n]-arene and cyclodextrin host …
energies. The challenge focused on macrocycles from pillar [n]-arene and cyclodextrin host …
What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling
S Khuttan, E Gallicchio - Journal of Chemical Theory and …, 2024 - ACS Publications
We introduce the self-relative binding free energy (self-RBFE) approach to evaluate the
intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The …
intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The …
Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and …
The first-and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors
(INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the …
(INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the …
Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host–guest systems
Z Sun, P Procacci - Physical Chemistry Chemical Physics, 2024 - pubs.rsc.org
As a contribution to the understanding and rationalization of methodological and modeling
effects in recent host–guest SAMPL challenges, using an alchemical molecular dynamics …
effects in recent host–guest SAMPL challenges, using an alchemical molecular dynamics …
[HTML][HTML] STORMM: Structure and topology replica molecular mechanics for chemical simulations
The Structure and TOpology Replica Molecular Mechanics (STORMM) code is a next-
generation molecular simulation engine and associated libraries optimized for performance …
generation molecular simulation engine and associated libraries optimized for performance …
Prediction of binding affinity and enthalpy of CB7 with alkaloids by attach-pull-release molecular dynamics simulations study
X Wu, L Wang, Y Qin, Y Gao, M Yang, P Cao… - Journal of Molecular …, 2024 - Elsevier
Host-guest complex has attracted much attention because of their fantastic capability.
Accurate prediction of their binding affinity and enthalpy is essential to the rational design of …
Accurate prediction of their binding affinity and enthalpy is essential to the rational design of …
Potential Distribution Theory of Alchemical Transfer
S Azimi, E Gallicchio - arXiv preprint arXiv:2407.14713, 2024 - arxiv.org
We present an analytical description of the Alchemical Transfer Method (ATM) for molecular
binding using the Potential Distribution Theory (PDT) formalism. ATM models the binding …
binding using the Potential Distribution Theory (PDT) formalism. ATM models the binding …
Evaluating the Reliability and Accuracy of Alchemical Binding Free Energy Methods and Calculations
F Sheenam - 2024 - academicworks.cuny.edu
Molecular recognition plays a crucial role in various biological processes, such as enzymatic
reactions, signal transduction, and genetic information processing. Investigating how …
reactions, signal transduction, and genetic information processing. Investigating how …
Chemical accuracy for ligand-receptor binding Gibbs energies through multi-level SQM/QM calculations
Calculating the Gibbs energies of binding of ligand-receptor systems with a thermochemical
accuracy of±1 kcal/mol is challenge to computational approaches. A semi-empirical …
accuracy of±1 kcal/mol is challenge to computational approaches. A semi-empirical …