ArticleJournal of chemical theory and computation2021
Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- NEMAT: An Automated Nonequilibrium Free-Energy Framework for Predicting Ligand Affinity in Membrane Proteins.Journal of chemical information and modeling · 2026Article
- Evolutionary Constraints Guide AlphaFold2 in Predicting Alternative Conformations and Inform Rational Mutation Design.Journal of chemical information and modeling · 2025Article
- Discovery of broad-spectrum antivirals targeting viral proteases using in silico structural modeling and cellular analysis.Antiviral research · 2025Article
- Searching for potential acetylcholinesterase inhibitors: a combined approach of multi-step similarity search, machine learning and molecular dynamics simulations.Royal Society open science · 2024Article
- Application of an alchemical free energy method for the prediction of thermostable DuraPETase variants.Applied microbiology and biotechnology · 2024Article
- Sustained antiviral insulin signaling during West Nile virus infection results in viral mutations.Frontiers in cellular and infection microbiology · 2024Article
- Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions.Journal of chemical theory and computation · 2023Article
- Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex.Journal of chemical theory and computation · 2023Article
- A FRET-Based Assay for the Identification of PCNA Inhibitors.International journal of molecular sciences · 2023Article
- Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex.bioRxiv : the preprint server for biology · 2023Article
- Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods.The journal of physical chemistry. B · 2023Article
- Assessment of a Computational Approach to Predict Drug Resistance Mutations for HIV, HBV and SARS-CoV-2.Molecules (Basel, Switzerland) · 2022Article
- Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers.Journal of chemical theory and computation · 2022Article
- Thermodynamics and kinetics in antibody resistance of the 501Y.V2 SARS-CoV-2 variant.RSC advances · 2021Article
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3 authors.
Funding
Abstract
Protein-protein binding is fundamental to most biological processes. It is important to be able to use computation to accurately estimate the change in protein-protein binding free energy due to mutations in order to answer biological questions that would be experimentally challenging, laborious, or time-consuming. Although nonrigorous free-energy methods are faster, rigorous alchemical molecular dynamics-based methods are considerably more accurate and are becoming more feasible with the advancement of computer hardware and molecular simulation software. Even with sufficient computational resources, there are still major challenges to using alchemical free-energy methods for protein-protein complexes, such as generating hybrid structures and topologies, maintaining a neutral net charge of the system when there is a charge-changing mutation, and setting up the simulation. In the current study, we have used the
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