End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.
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Summary
In this review, methods to adjust the polar solvation energy and to improve the performance of MM/PBSA and MM/GBSA calculations are reviewed and discussed and guidance is provided for practically applying these methods in drug design and related research fields.
- Type
- review
- Published
- 2019-06-24
- Cited by
- 1,924
- References
- 371
- OpenAlex
- https://openalex.org/W2954094311
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:195696542
Keywords
Chemistry, Drug, Point (geometry), Nanotechnology, Biochemical engineering
References
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- Impact of peripheral mutations on the access channels of human cytochrome P450 1A2
- The guanidiniocarbonylpyrrole–fluorophore conjugates as theragnostic tools for dipeptidyl peptidase III monitoring and inhibition
- New application of in silico methods in identifying mechanisms of action and key components of anti-cancer herbal formulation YIV-906 (PHY906).
- Computer-aided rational design of acyclovir analogs to inhibit purine nucleoside phosphorylase
- Computational investigation of a ternary model of SnoN-SMAD3-SMAD4 complex
- Probing the Druggablility on the Interface of the Protein–Protein Interaction and Its Allosteric Regulation Mechanism on the Drug Screening for the CXCR4 Homodimer
- Computational insights into the binding pattern of mitochondrial calcium uniporter inhibitor through homology modeling, molecular dynamics simulation, binding free energy prediction and density functional theory calculation
- GroScore: Accurate Scoring of Protein-Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations
- Applicability and performance of linear interaction energy based binding affinity calculation
- Identify old drugs as selective bacterial β‐GUS inhibitors by structural‐based virtual screening and bio‐evaluations
- Molecular Basis for Metabolic Regioselectivity and Mechanism of Cytochrome P450s toward Carcinogenic 4-(Methylnitrosamino)-(3-pyridyl)-1-butanone (NNK).
- Dimerization energetics of the G‐protein coupled bile acid receptor TGR5 from all‐atom simulations
- Calculating the absolute binding free energy of the insulin dimer in an explicit solvent
- Identification of Potential Inhibitors from Traditional Chinese Medicine for Fibroblast Growth Factor Receptor 1 Based on Virtual Screening and Molecular Dynamics Analysis
- Exploration of the selective binding mechanism of GSK3β via molecular modeling and molecular dynamics simulation studies
- Novel MscL agonists that allow multiple antibiotics cytoplasmic access activate the channel through a common binding site
- The binding mode of vilazodone in the human serotonin transporter elucidated by ligand docking and molecular dynamics simulations.
- Improving the performance of the MM/PBSA and MM/GBSA methods in recognizing the native structure of the Bcl-2 family using the interaction entropy method.
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