ArticleBiochimica et biophysica acta2015
Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design.
Article in Biochimica et biophysica acta, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed, 84 citations in OpenAlex.
- Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model.Journal of chemical theory and computation · 2026Article
- Unveiling Anti-Cancer Potential through ADMET Prediction, Molecular Docking, Molecular Dynamics, andCurrent topics in medicinal chemistry · 2026Article
- Transferable Machine Learning Interatomic Potential for Bond Dissociation Energy Prediction of Drug-like Molecules.Journal of chemical theory and computation · 2024Article
- Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field.Journal of chemical theory and computation · 2023Article
- Article
- Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid.Journal of computer-aided molecular design · 2022Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.Journal of chemical theory and computation · 2020Article
- Optimization of Protein-Ligand Electrostatic Interactions Using an Alchemical Free-Energy Method.Journal of chemical theory and computation · 2019Article
- Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields.MedChemComm · 2019Article
- New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy.RSC advances · 2019Article
- Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction.Chemical communications (Cambridge, England) · 2017Article
- Predicting Binding Free Energies: Frontiers and Benchmarks.Annual review of biophysics · 2017Review
- Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.Journal of chemical theory and computation · 2016Article
- Disorder-to-Order Transition of an Active-Site Loop Mediates the Allosteric Activation of Sortase A.Biophysical journal · 2015Article
- Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.PLoS computational biology · 2015Article
- Homologous ligands accommodated by discrete conformations of a buried cavity.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundNon-nucleoside inhibitors of HIV reverse transcriptase are an important component of treatment against HIV infection. Novel inhibitors are sought that increase potency against variants that contain the Tyr181Cys mutation.
methodsMolecular dynamics based free energy perturbation simulations have been run to study factors that contribute to protein-ligand binding, and the results are compared with those from previous Monte Carlo based simulations and activity data.
resultsPredictions of protein-ligand binding modes are very consistent for the two simulation methods; the accord is attributed to the use of an enhanced sampling protocol. The Tyr181Cys binding pocket supports large, hydrophobic substituents, which is in good agreement with experiment.
conclusionsAlthough some discrepancies exist between the results of the two simulation methods and experiment, free energy perturbation simulations can be used to rapidly test small molecules for gains in binding affinity. GENERAL SIGNIFICANCE: Free energy perturbation methods show promise in providing fast, reliable and accurate data that can be used to complement experiment in lead optimization projects. This article is part of a Special Issue entitled "Recent developments of molecular dynamics".
Indexed as
Identifiers
What OpenQuestion holds
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.