Article

Binding Affinity Estimation from Restrained Umbrella Sampling Simulations

2022-08-01

Abstract excerpt

<title>Abstract</title> <p>The protein-ligand binding affinity quantifies the binding strength between a protein and its ligand. Computer modeling and simulations can be used to estimate the binding affinity or binding free energy using data- or physics-driven methods or a combination thereof. Here, we discuss a purely physics-based sampling approach based on biased molecular dynamics (MD) simulations. Our propos...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 2e333cab-59f1-507e-ac6b-4546a21048f0
DOI: 10.21203/rs.3.rs-1443106/v1

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Binding Affinity Estimation from Restrained Umbrella Sampling SimulationsDOI 10.21203/rs.3.rs-1443106/v1Read

Binding Affinity Estimation From Restrained Umbrella Sampling SimulationsSemantic proximity Read

Computer-guided Binding Mode Identification and Affinity Improvement of an LRR Protein Binder without Structure DeterminationSemantic proximity Read

Protein-protein interactions: scoring schemes and binding affinity.Semantic proximity Read

Cost function network-based design of protein-protein interactions: predicting changes in binding affinity.Semantic proximity Read

Free Energy Calculations for Protein-Ligand Binding Prediction.Semantic proximity Read

Biophysical Inference of Epistasis and the Effects of Mutations on Protein Stability and Function.Semantic proximity Read

Pose-Rescorer: A Deterministic Single-Frame MM/GBSA Workflow for Post-Docking Ligand RankingSemantic proximity Read

Limiting assumptions in structure-based design: binding entropy.Semantic proximity Read

Fast and reliable prediction of domain-peptide binding affinity using coarse-grained structure models.Semantic proximity Read

Elucidating Electronic Structure Variations in Nucleic Acid-Protein Complexes Involved in Transcription Regulation Using a Tight-Binding ApproachSemantic proximity Read

Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with ExperimentSemantic proximity Read

Reliable <i>in silico</i> ranking of engineered therapeutic TCR binding affinities with MMPB/GBSASemantic proximity Read