ArticleJournal of computational chemistry2015
Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI).
Article in Journal of computational chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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49 citing papers in PubMed, 126 citations in OpenAlex.
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- Discovery and optimization of a guanylhydrazone-based small molecule to replace bFGF for cell culture applications.Biochemistry and biophysics reports · 2025Article
- In Silico ADME Methods Used in the Evaluation of Natural Products.Pharmaceutics · 2025Review
- Effects of Conformational Sampling on Computing Redox Properties Using Linear Response Approach.The journal of physical chemistry. B · 2025Article
- Discovery of novel acetylcholinesterase inhibitors through AI-powered structure prediction and high-performance computing-enhanced virtual screening.RSC advances · 2025Article
- Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum.Nucleic acids research · 2025Article
- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- A head-to-head comparison of MM/PBSA and MM/GBSA in predicting binding affinities for the CBJournal of molecular modeling · 2024Article
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- CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes.Journal of chemical information and modeling · 2023Article
- Self-Assembly of Insulin-Derived Chimeric Peptides into Two-Component Amyloid Fibrils: The Role of Coulombic Interactions.The journal of physical chemistry. B · 2023Article
- 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
- Structure-based approach: molecular insight of pyranocumarins against α-glucosidase through computational studies.RSC advances · 2023Article
- Prioritizing Small Sets of Molecules for Synthesis through in-silico Tools: A Comparison of Common Ranking Methods.ChemMedChem · 2023Article
- Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations.Journal of computer-aided molecular design · 2023Article
- Modeling of Transmembrane Domain and Full-Length TLRs in Membrane Models.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant.Journal of computer-aided molecular design · 2022Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
To validate a method for predicting the binding affinities of FabI inhibitors, three implicit solvent methods, MM-PBSA, MM-GBSA, and QM/MM-GBSA were carefully compared using 16 benzimidazole inhibitors in complex with Francisella tularensis FabI. The data suggests that the prediction results are sensitive to radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length, if only one simulation trajectory is used for each ligand. In this case, QM/MM-GBSA using 6 ns MD simulation trajectories together with GB(neck2) , PM3, and the mbondi2 radii set, generate the closest agreement with experimental values (r(2) = 0.88). However, if the three implicit solvent methods are averaged from six 1 ns MD simulations for each ligand (called "multiple independent sampling"), the prediction results are relatively insensitive to all the tested parameters. Moreover, MM/GBSA together with GB(HCT) and mbondi, using 600 frames extracted evenly from six 0.25 ns MD simulations, can also provide accurate prediction to experimental values (r(2) = 0.84). Therefore, the multiple independent sampling method can be more efficient than a single, long simulation method. Since future scaffold expansions may significantly change the benzimidazole's physiochemical properties (charges, etc.) and possibly binding modes, which may affect the sensitivities of various parameters, the relatively insensitive "multiple independent sampling method" may avoid the need of an entirely new validation study. Moreover, due to large fluctuating entropy values, (QM/)MM-P(G)BSA were limited to inhibitors' relative affinity prediction, but not the absolute affinity. The developed protocol will support an ongoing benzimidazole lead optimization program.
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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.