ArticleJournal of chemical theory and computation2011
Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model.
Article in Journal of chemical theory and computation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed.
- Insight into the Binding Interaction between PEDCs and hERRγ Utilizing Molecular Docking and Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2024Article
- Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant.The journal of physical chemistry. B · 2023Article
- MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Journal of computer-aided molecular design · 2023Article
- Anticancer potential of β-sitosterol and oleanolic acid as through inhibition of human estrogenic 17beta-hydroxysteroid dehydrogenase type-1 based on anRSC advances · 2022Article
- Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: molecular docking and molecular dynamics simulations.Journal of biomolecular structure & dynamics · 2022Article
- Exploring the Binding Mechanism of a Supramolecular Tweezer CLR01 to 14-3-3σ ProteinFrontiers in chemistry · 2022Article
- Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies.Journal of chemical information and modeling · 2019Article
- The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction.Structural dynamics (Melville, N.Y.) · 2018Article
- Extended Concerted Rotation Technique Enhances the Sampling Efficiency of the Computational Peptide-Design Algorithm.Journal of chemical theory and computation · 2017Article
- Simulation study of the ability of a computationally-designed peptide to recognize target tRNAProtein science : a publication of the Protein Society · 2016Article
- Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned λ N peptide binds boxB RNA.Journal of computational chemistry · 2016Article
- The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.Expert opinion on drug discovery · 2015Review
- Structure-based virtual screening for drug discovery: principles, applications and recent advances.Current topics in medicinal chemistry · 2014Review
- Contributions of the RAD51 N-terminal domain to BRCA2-RAD51 interaction.Nucleic acids research · 2013Article
- Fragment-based drug discovery using a multidomain, parallel MD-MM/PBSA screening protocol.Journal of chemical information and modeling · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
A variable dielectric model based on residue types for better description of protein-ligand electrostatics in MM-GBSA scoring is reported. The variable dielectric approach provides better correlation with binding data and reduces the score dynamic range, typically observed in the standard MM-GB/SA method. The latter supports the view that exaggerated enthalpic separation between weak and potent compounds due to the lack of shielding effects in the model is greatly responsible for the wide scoring spread.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.