ArticleJournal of chemical information and modeling2011
Solvent interaction energy calculations on molecular dynamics trajectories: increasing the efficiency using systematic frame selection.
Article in Journal of chemical information and modeling, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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Who cites it
11 citing papers in PubMed.
- Targeting SARS-CoV-2 main protease: a pharmacophore and molecular modeling approach.Journal of molecular modeling · 2025Article
- First report on chemometrics-driven multilayered lead prioritization in addressing oxysterol-mediated overexpression of G protein-coupled receptor 183.Molecular diversity · 2024Article
- Dissecting the Structural Dynamics of Authentic Cholesteryl Ester Transfer Protein for the Discovery of Potential Lead Compounds: A Theoretical Study.International journal of molecular sciences · 2023Article
- Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants.Scientific reports · 2022Article
- Structural, energetic and lipophilic analysis of SARS-CoV-2 non-structural protein 9 (NSP9).Scientific reports · 2021Article
- Article
- Structure-Based Virtual Screening, Molecular Dynamics and Binding Free Energy Calculations of Hit Candidates as ALK-5 Inhibitors.Molecules (Basel, Switzerland) · 2020Article
- Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.Journal of chemical information and modeling · 2013Article
- Article
- Variability in docking success rates due to dataset preparation.Journal of computer-aided molecular design · 2012Article
- Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction.Journal of computer-aided molecular design · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
End-point methods such as linear interaction energy (LIE) analysis, molecular mechanics generalized Born solvent-accessible surface (MM/GBSA), and solvent interaction energy (SIE) analysis have become popular techniques to calculate the free energy associated with protein-ligand binding. Such methods typically use molecular dynamics (MD) simulations to generate an ensemble of protein structures that encompasses the bound and unbound states. The energy evaluation method (LIE, MM/GBSA, or SIE) is subsequently used to calculate the energy of each member of the ensemble, thus providing an estimate of the average free energy difference between the bound and unbound states. The workflow requiring both MD simulation and energy calculation for each frame and each trajectory proves to be computationally expensive. In an attempt to reduce the high computational cost associated with end-point methods, we study several methods by which frames may be intelligently selected from the MD simulation including clustering and address the question of how the number of selected frames influences the accuracy of the SIE calculations.
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Registered trials
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