ArticleACS omega2019
Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method.
Article in ACS omega, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Rapid clearance of achiral small-molecule drugs using de novo-designed proteins and their cyclic and mirror-image variants.Nature biomedical engineering · 2025Article
- Simultaneous Construction of Free Energy Surfaces via Multisite λ Dynamics and Umbrella Sampling.Journal of chemical theory and computation · 2025Article
- High-throughput virtual screening of potential inhibitors of GPR52 using docking and biased sampling method for Huntington's disease therapy.Molecular diversity · 2024Article
- Optimizing Phosphopeptide Structures That Target 14-3-3ε in Cutaneous Squamous Cell Carcinoma.ACS omega · 2024Article
- The Application of MD Simulation to Lead Identification, Vaccine Design, and Structural Studies in Combat against Leishmaniasis - A Review.Mini reviews in medicinal chemistry · 2024Review
- Molecular basis and cellular functions of vinculin-actin directional catch bonding.Nature communications · 2023Article
- Optimizing Phosphopeptide Structures That Target 14-3-3ε in Cutaneous Squamous Cell Carcinoma.bioRxiv : the preprint server for biology · 2023Article
- Effect of Colchicine Binding Site Inhibitors on the Tubulin Intersubunit Interaction.ACS omega · 2023Article
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- Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors.Molecules (Basel, Switzerland) · 2023Article
- Computational Approaches to the Rational Design of Tubulin-Targeting Agents.Biomolecules · 2023Review
- Computational Evaluation of Peptide-Protein Binding Affinities: Application of Potential of Mean Force Calculations to SH2 Domains.Methods in molecular biology (Clifton, N.J.) · 2023Article
- CHAPERONComputational and structural biotechnology journal · 2023Article
- Binding Studies and Lead Generation of Pteridin-7(8International journal of molecular sciences · 2022Article
- Benchmarking the ability of novel compounds to inhibit SARS-CoV-2 main protease using steered molecular dynamics simulations.Computers in biology and medicine · 2022Article
- Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD.Materials (Basel, Switzerland) · 2022Article
- In silico screening of potential β-secretase (BACE1) inhibitors from VIETHERB database.Journal of molecular modeling · 2022Article
- Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 MRSC advances · 2022Article
- Umbrella Sampling-Based Method to Compute Ligand-Binding Affinity.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Unbinding ligands from SARS-CoV-2 Mpro via umbrella sampling simulations.Royal Society open science · 2022Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The binding between two biomolecules is one of the most critical factors controlling many bioprocesses. Therefore, it is of great interest to derive a reliable method to calculate the free binding energy between two biomolecules. In this work, we have demonstrated that the binding affinity of ligands to proteins can be determined through biased sampling simulations. The umbrella sampling (US) method was applied on 20 protein-ligand complexes, including the cathepsin K (CTSK), type II dehydroquinase (DHQase), heat shock protein 90 (HSP90), and factor Xa (FXa) systems. The ligand-binding affinity was evaluated as the difference between the largest and smallest values of the free-energy curve, which was obtained via a potential of mean force analysis. The calculated affinities differ sizably from the previously reported experimental values, with an average difference of ∼3.14 kcal/mol. However, the calculated results are in good correlation with the experimental data, with correlation coefficients of 0.76, 0.87, 0.96, and 0.97 for CTSK, DHQase, HSP90, and FXa, respectively. Thus, the binding free energy of a new ligand can be reliably estimated using our US approach. Furthermore, the root-mean-square errors (RMSEs) of binding affinity of these systems are 1.13, 0.90, 0.37, and 0.25 kcal/mol, for CTSK, DHQase, HSP90, and FXa, respectively. The small RMSE values indicate the good precision of the biased sampling method that can distinguish the ligands exhibiting similar binding affinities.
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