ArticleJournal of molecular biology2017
Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1.
Article in Journal of molecular biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- A Functional Investigation of Antibody Fc-FcRn Variant Binding Guided by In Silico Free Energy Perturbation Methods.Journal of molecular biology · 2026Article
- Chemical neighborhood exploration for substrate discovery in biocatalysis.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A functional investigation of antibody Fc-FcRn variant binding guided bybioRxiv : the preprint server for biology · 2026Article
- Antibody Affinity Maturation by Computational Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Ensemble molecular mimicry correlates with antibody cross-reactivity in proteome-wide studies.Frontiers in immunology · 2026Article
- Integration of Experimental and Computational Methods to Characterize Glycoproteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein-Ligand Binding.Journal of chemical theory and computation · 2024Article
- Robust Prediction of Relative Binding Energies for Protein-Protein Complex Mutations Using Free Energy Perturbation Calculations.Journal of molecular biology · 2024Article
- Understanding the impact of binding free energy and kinetics calculations in modern drug discovery.Expert opinion on drug discovery · 2024Review
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- Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations.bioRxiv : the preprint server for biology · 2024Article
- An Ensemble Docking Approach for Analyzing and Designing Aptamer Heterodimers Targeting VEGFInternational journal of molecular sciences · 2024Article
- Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Alchemical Free Energy Calculations on Membrane-Associated Proteins.Journal of chemical theory and computation · 2023Review
- 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
- 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
- Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction.RSC chemical biology · 2023Review
- Role of Dynamics and Mutations in Interactions of a Zinc Finger Antiviral Protein with CG-rich Viral RNA.Journal of chemical information and modeling · 2023Article
- Target-template relationships in protein structure prediction and their effect on the accuracy of thermostability calculations.Protein science : a publication of the Protein Society · 2023Article
- Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods.The journal of physical chemistry. B · 2023Article
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14 authors.
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Abstract
Direct calculation of relative binding affinities between antibodies and antigens is a long-sought goal. However, despite substantial efforts, no generally applicable computational method has been described. Here, we describe a systematic free energy perturbation (FEP) protocol and calculate the binding affinities between the gp120 envelope glycoprotein of HIV-1 and three broadly neutralizing antibodies (bNAbs) of the VRC01 class. The protocol has been adapted from successful studies of small molecules to address the challenges associated with modeling protein-protein interactions. Specifically, we built homology models of the three antibody-gp120 complexes, extended the sampling times for large bulky residues, incorporated the modeling of glycans on the surface of gp120, and utilized continuum solvent-based loop prediction protocols to improve sampling. We present three experimental surface plasmon resonance data sets, in which antibody residues in the antibody/gp120 interface were systematically mutated to alanine. The RMS error in the large set (55 total cases) of FEP tests as compared to these experiments, 0.68kcal/mol, is near experimental accuracy, and it compares favorably with the results obtained from a simpler, empirical methodology. The correlation coefficient for the combined data set including residues with glycan contacts, R
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