Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations.

Jared M Sampson Daniel A CannonJianxin DuanJordan C K EpsteinAlina P Sergeeva Phinikoula S KatsambaSeetha M MannepalliFabiana A BahnaHélène Adihou Stéphanie M Guéret Ranganath Gopalakrishnan Stefan Geschwindner D Gareth Rees Anna Sigurdardottir Trevor Wilkinson Roger B Dodd Leonardo De Maria Juan Carlos Mobarec Lawrence Shapiro Barry Honig Andrew Buchanan Richard A Friesner Lingle Wang

Published in: bioRxiv : the preprint server for biology (2024)

Reliable calculation of relative binding free energy changes for most protein mutations to within ∼1 kcal/mol.Automated Protein FEP+ Groups treatment of alternate protonation states for titratable residues.Application of FEP+ methodology to "real-world" protein design projects.

Keyphrases

protein protein
small molecule
binding protein
density functional theory
amino acid
machine learning
high throughput
molecular dynamics
dna binding
transcription factor
quality improvement
smoking cessation