ArticleJournal of chemical information and modeling2019
Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations.
Article in Journal of chemical information and modeling, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Temperature-Dependent Menthol Binding across TRPM8 Conformational States.Journal of the American Chemical Society · 2026Article
- Mixed-Solvent MD suite: modular tools for building and analyzing mixed-solvent molecular dynamics systems.Journal of computer-aided molecular design · 2026Article
- Computational approaches to druggable site identification: Current status and future perspective.Acta pharmaceutica Sinica. B · 2026Review
- Chasing allosteric inhibition of the SARS-CoV-2 PLpro via molecular dynamics simulations with flooding fragments (MDFFr).Journal of computer-aided molecular design · 2025Article
- Enhancing SILCS-MC via GPU Acceleration and Ligand Conformational Optimization with Genetic and Parallel Tempering Algorithms.The journal of physical chemistry. B · 2024Article
- AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics.Journal of chemical information and modeling · 2023Article
- Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth.Journal of chemical theory and computation · 2022Article
- Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes.International journal of molecular sciences · 2022Article
- Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease.Journal of chemical information and modeling · 2022Article
- Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.New journal of chemistry = Nouveau journal de chimie · 2022Article
- Concentration-dependent thermodynamic analysis of the partition process of small ligands into proteins.Computational and structural biotechnology journal · 2022Article
- Impact of electronic polarizability on protein-functional group interactions.Physical chemistry chemical physics : PCCP · 2020Article
- Investigating Cryptic Binding Sites by Molecular Dynamics Simulations.Accounts of chemical research · 2020Review
- Allosteric Binding Sites On Nuclear Receptors: Focus On Drug Efficacy and Selectivity.International journal of molecular sciences · 2020Article
- AnalyzingFrontiers in molecular biosciences · 2020Article
- Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions.Computational and structural biotechnology journal · 2020Article
- Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations.Protein science : a publication of the Protein Society · 2020Article
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Authors and funding
3 authors.
Funding
Abstract
In our recent efforts to map protein surfaces using mixed-solvent molecular dynamics (MixMD) (Ghanakota, P.; Carlson, H. A. Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems. J. Phys. Chem. B 2016, 120, 8685-8695), we were able to successfully capture active sites and allosteric sites within the top-four most occupied hotspots. In this study, we describe our approach for estimating the thermodynamic profile of the binding sites identified by MixMD. First, we establish a framework for calculating free energies from MixMD simulations, and we compare our approach to alternative methods. Second, we present a means to obtain a relative ranking of the binding sites by their configurational entropy. The theoretical maximum and minimum free energy and entropy values achievable under such a framework along with the limitations of the techniques are discussed. Using this approach, the free energy and relative entropy ranking of the top-four MixMD binding sites were computed and analyzed across our allosteric protein targets: Abl Kinase, Androgen Receptor, Pdk1 Kinase, Farnesyl Pyrophosphate Synthase, Chk1 Kinase, Glucokinase, and Protein Tyrosine Phosphatase 1B.
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