ArticleScientific reports2022
Large-scale application of free energy perturbation calculations for antibody design.
Article in Scientific reports, 2022. 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.
- A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation.iScience · 2026Article
- Antibody Affinity Maturation by Computational Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Optimizing the breadth of SARS-CoV-2-neutralizing antibodies in vivo and in silico.Human vaccines & immunotherapeutics · 2025Review
- Therapeutic Effect of a Recombinant Human Fibronectin Construct in Skeletal Muscle Repair and Oxidative Stress.International journal of molecular sciences · 2025Article
- Real-Time Affinity Measurements of Proteins Synthesized in Cell-Free Lysate Using Fluorescence Correlation Spectroscopy.Analytical chemistry · 2025Article
- In silico prediction of GRP78-CRIPTO binding sites to improve therapeutic targeting in glioblastoma.Scientific reports · 2025Article
- Preemptive optimization of a clinical antibody for broad neutralization of SARS-CoV-2 variants and robustness against viral escape.Science advances · 2025Article
- Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method.BMC bioinformatics · 2024Article
- Understanding the impact of binding free energy and kinetics calculations in modern drug discovery.Expert opinion on drug discovery · 2024Review
- Article
- Surfaces: a software to quantify and visualize interactions within and between proteins and ligands.Bioinformatics (Oxford, England) · 2023Article
- Accurate and Efficient Multilevel Free Energy Simulations with Neural Network-Assisted Enhanced Sampling.Journal of chemical theory and computation · 2023Article
- Article
- In Silico Maturation of a Nanomolar Antibody against the Human CXCR2.Biomolecules · 2022Article
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9 authors.
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Abstract
Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate the free energy difference between distinct chemical systems. Here we report our implementation of automated large-scale FEP calculations, using the Amber software package, to facilitate antibody design and evaluation. In combination with Hamiltonian replica exchange, our FEP simulations aim to predict the effect of mutations on both the binding affinity and the structural stability. Importantly, we incorporate multiple strategies to faithfully estimate the statistical uncertainties in the FEP results. As a case study, we apply our protocols to systematically evaluate variants of the m396 antibody for their conformational stability and their binding affinity to the spike proteins of SARS-CoV-1 and SARS-CoV-2. By properly adjusting relevant parameters, the particle collapse problems in the FEP simulations are avoided. Furthermore, large statistical errors in a small fraction of the FEP calculations are effectively reduced by extending the sampling, such that acceptable statistical uncertainties are achieved for the vast majority of the cases with a modest total computational cost. Finally, our predicted conformational stability for the m396 variants is qualitatively consistent with the experimentally measured melting temperatures. Our work thus demonstrates the applicability of FEP in computational antibody design.
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