Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy.

Journal of chemical theory and computation - 13 Apr 2021

Patel Dharmeshkumar, Patel Jagdish Suresh, Ytreberg F Marty

Abstract excerpt

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...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Models, Molecular
Share to Mutation
Share to Protein Binding

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to Proteins

Share to Thermodynamics

Source

Open in PubMed Open full text

Identifiers

PMID: 33709712
DOI: 10.1021/acs.jctc.0c01045
PMCID: PMC8044032

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 2 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy.PMID 33709712Read ↗

Calculation of binding free energies.Semantic proximity Read ↗

Assessment of software methods for estimating protein-protein relative binding affinities.Semantic proximity Read ↗

Alchemical Calculation of Relative Free Energies for Charge-Changing Mutations at Protein-Protein Interfaces Considering Fixed and Variable Protonation States.Semantic proximity Read ↗

Improvement in predicting drug sensitivity changes associated with protein mutations using a molecular dynamics based alchemical mutation method.Semantic proximity Read ↗

Accurate Prediction of Protein Thermodynamic Stability Changes upon Residue Mutation using Free Energy Perturbation.Semantic proximity Read ↗

Inferring the microscopic surface energy of protein-protein interfaces from mutation data.Semantic proximity Read ↗

Software for Predicting Binding Free Energy of Protein-Protein Complexes and Their Mutants.Semantic proximity Read ↗

Robust Prediction of Relative Binding Energies for Protein-Protein Complex Mutations Using Free Energy Perturbation Calculations.Semantic proximity Read ↗

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.Semantic proximity Read ↗

Nonbonded Force Field Parameters from MBIS Partitioning of the Molecular Electron Density Improve Binding Affinity Predictions of the T4-Lysozyme Double Mutant.Semantic proximity Read ↗

Mechanisms of protein-ligand association and its modulation by protein mutations.Semantic proximity Read ↗

Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA Complexes.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.