ArticleBiophysics and physicobiology2021
Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model.
Article in Biophysics and physicobiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
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- A novel mRNA-based multi-epitope vaccine for rabies virus computationally designed via reverse vaccinology and immunoinformatics.Scientific reports · 2025Article
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
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- Design a multi-epitope vaccine candidate against Acinetobacter baumannii using advanced computational methods.AMB Express · 2025Article
- PLAIG: Protein-Ligand Binding Affinity Prediction Using a Novel Interaction-Based Graph Neural Network Framework.ACS bio & med chem Au · 2025Article
- Predicting Protein-Ligand Binding Affinity Using Fusion Model of Spatial-Temporal Graph Neural Network and 3D Structure-Based Complex Graph.Interdisciplinary sciences, computational life sciences · 2025Article
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- Anticancer Potential of Quercetin on Oral Squamous Cell Carcinoma: A Scoping Review and Molecular Docking.European journal of dentistry · 2025Article
- Investigation into in silico and in vitro approaches for inhibitors targeting MCM10 in Leishmania donovani: a comprehensive study.Molecular diversity · 2025Article
- Anti-Tyrosinase and Radical Scavenging Activities of Selected Cassipourea Plants and Isolated 7-Methoxygeranin A: Traditional Use as Skin Lighteners.Journal of experimental pharmacology · 2025Article
- Identification of Potential Inhibitors of Three NDM Variants ofCurrent computer-aided drug design · 2025Article
- Bioprospection ofInternational journal of medical sciences · 2025Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We recently proposed a computational procedure to simulate the dissociation of protein/ligand complexes using the dissociation Parallel Cascade Selection Molecular Dynamics simulation (dPaCS-MD) method and to analyze the generated trajectories using the Markov state model (MSM). This procedure, called dPaCS-MD/MSM, enables calculation of the dissociation free energy profile and the standard binding free energy. To examine whether this method can reproduce experimentally determined binding free energies for a variety of systems, we used it to investigate the dissociation of three protein/ligand complexes: trypsin/benzamine, FKBP/FK506, and adenosine A
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