ArticleJournal of chemical theory and computation2018
Fast Calculation of Protein-Protein Binding Free Energies Using Umbrella Sampling with a Coarse-Grained Model.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
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- Advances in molecular dynamics approaches for investigating cell-penetrating peptides.Biophysical reviews · 2026Review
- Assessing Computational Strategies for the Evaluation of Antibody Binding Affinities.Journal of chemical theory and computation · 2025Article
- Binding of SARS-CoV-1/2 NSP1 to DNA Polymerase α-Primase Inhibits DNA Replication through Reduction of Interaction between DNA and DNA Polymerase α-Primase.Journal of chemical information and modeling · 2025Article
- Unravelling the human taste receptor interactome: machine learning and molecular modelling insights into protein-protein interactions.NPJ science of food · 2025Article
- Interface integrity in septin protofilaments is maintained by an arginine residue conserved from yeast to man.Molecular biology of the cell · 2025Article
- Biophysics of SARS-CoV-2 spike protein's receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights.Biophysical reviews · 2025Review
- Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation.The journal of physical chemistry. B · 2024Article
- Artificial Intelligence-Powered Molecular Docking and Steered Molecular Dynamics for Accurate scFv Selection of Anti-CD30 Chimeric Antigen Receptors.International journal of molecular sciences · 2024Article
- Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins.Journal of chemical information and modeling · 2023Article
- Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants.Colloids and surfaces. B, Biointerfaces · 2023Article
- In Silico Maturation of a Nanomolar Antibody against the Human CXCR2.Biomolecules · 2022Article
- Wetting Properties of Clathrate Hydrates in the Presence of Polycyclic Aromatic Compounds: Evidence of Ion-Specific Effects.The journal of physical chemistry letters · 2022Article
- Antibody-nanobody combination increases their neutralizing activity against SARS-CoV-2 and nanobody H11-H4 is effective against Alpha, Kappa and Delta variants.Scientific reports · 2022Article
- Communication pathways bridge local and global conformations in an IgG4 antibody.Scientific reports · 2021Article
- Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue.Journal of chemical theory and computation · 2021Article
- Deep geometric representations for modeling effects of mutations on protein-protein binding affinity.PLoS computational biology · 2021Article
- Physical constraints and functional plasticity of cellulases.Nature communications · 2021Article
- Unusual RNA binding of FUS RRM studied by molecular dynamics simulation and enhanced sampling method.Biophysical journal · 2021Article
- Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy.Journal of chemical theory and computation · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Determination of protein-protein binding affinity values is key to understanding various underlying biological phenomena, such as how missense variations change protein-protein binding. Most existing non-rigorous (fast) and rigorous (slow) methods that rely on all-atom representation of the proteins force the user to choose between speed and accuracy. In an attempt to achieve balance between speed and accuracy, we have combined rigorous umbrella sampling molecular dynamics simulation with a coarse-grained protein model. We predicted the effect of missense variations on binding affinity by selecting three protein-protein systems and comparing results to empirical relative binding affinity values and to non-rigorous modeling approaches. We obtained significant improvement both in our ability to discern stabilizing from destabilizing missense variations and in the correlation between predicted and experimental values compared to non-rigorous approaches. Overall our results suggest that using a rigorous affinity calculation method with coarse-grained protein models could offer fast and reliable predictions of protein-protein binding free energies.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.