ArticleJournal of chemical theory and computation2017
Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Prot-ΔΔG: Prediction of protein-protein binding affinity changes upon mutations with pre-training strategies.Journal of computer-aided molecular design · 2026Article
- Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field.Journal of chemical theory and computation · 2024Article
- Refinement of Docked Protein-Protein Complexes Using Repulsive Scaling Replica Exchange Simulations.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems.Journal of chemical information and modeling · 2023Article
- How does the same ligand activate signaling of different receptors in TNFR superfamily: a computational study.Journal of cell communication and signaling · 2023Article
- Computer aided drug design in the development of proteolysis targeting chimeras.Computational and structural biotechnology journal · 2023Review
- Absolute binding free energy calculations improve enrichment of actives in virtual compound screening.Scientific reports · 2022Article
- Computational Tools for Accurate Binding Free-Energy Prediction.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue.Journal of chemical theory and computation · 2021Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- Thermodynamics and Free Energy Landscape of BAR-Domain Dimerization from Molecular Simulations.The journal of physical chemistry. B · 2021Article
- Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest-Host Systems.Journal of chemical theory and computation · 2020Article
- Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions.Frontiers in physics · 2020Article
- On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.Journal of computational chemistry · 2020Article
- Calculating the absolute binding free energy of the insulin dimer in an explicit solvent.RSC advances · 2020Article
- iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations.Proteins · 2019Article
- Specific Residue Interactions Regulate the Binding of Dengue Antigens to Broadly Neutralizing EDE Antibodies.ChemistryOpen · 2018Article
- Lessons learned from merging wet lab experiments with molecular simulation to improve mAb humanization.Protein engineering, design & selection : PEDS · 2018Article
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2 authors.
Funding
Abstract
Virtually all biological processes depend on the interaction between proteins at some point. The correct prediction of biomolecular binding free-energies has many interesting applications in both basic and applied pharmaceutical research. While recent advances in the field of molecular dynamics (MD) simulations have proven the feasibility of the calculation of protein-protein binding free energies, the large conformational freedom of proteins and complex free energy landscapes of binding processes make such calculations a difficult task. Moreover, convergence and reversibility of resulting free-energy values remain poorly described. In this work, an easy-to-use, yet robust approach for the calculation of standard-state protein-protein binding free energies using perturbed distance restraints is described. In the binding process the conformations of the proteins were restrained, as suggested earlier. Two approaches to avoid end-state problems upon release of the conformational restraints were compared. The method was evaluated by practical application to a small model complex of ubiquitin and the very flexible ubiquitin-binding domain of human DNA polymerase ι (UBM2). All computed free energy differences were closely monitored for convergence, and the calculated binding free energies had a mean unsigned deviation of only 1.4 or 2.5 kJ·mol
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