ReviewExpert opinion on drug discovery2024
Understanding the impact of binding free energy and kinetics calculations in modern drug discovery.
Review in Expert opinion on drug discovery, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- In Silico Screening of Therapeutic Targets as a Tool to Optimize the Development of Drugs and Nutraceuticals in the Treatment of DiabetesInternational journal of molecular sciences · 2024Pooled it
- G12 mutations rewire allosteric communication at the Ras-RalGDS interface.Biophysical journal · 2026Article
- Discovery of ERα-Targeting Phytochemicals With In Vitro Cytotoxicity and Computational Prediction of Y537S Mutant Inhibition.Chemical biology & drug design · 2026Article
- Review
- Exploration of the mechanism of Xinjiang Rosa laxa Retz.Fruit extract on IgA nephropathy by bioinformatics and machine learning methods.Bioresources and bioprocessing · 2026Article
- Complement-Modulating Mechanisms of Ginkgo biloba Extract in Dry AMD: Insights From Molecular Docking and Dynamics Simulations.Translational vision science & technology · 2026Article
- Biophysical Sensing Tools in Drug Discovery: Integrating Kinetics, Thermodynamics, Cellular Target Engagement and Structure.Sensors (Basel, Switzerland) · 2026Review
- Efficient Binding Affinity Estimation for Fragment-Based Compounds Using a Separated Topologies Approach.Journal of chemical information and modeling · 2026Article
- A Mechanistic Digital Twin of uPAR-Driven Prostate Cancer Invasion Integrating ODE Signalling and Agent-Based Modelling.Pharmaceuticals (Basel, Switzerland) · 2026Article
- A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.Journal of chemical information and modeling · 2026Article
- Non-invasive pharmacological advances in early retinopathy treatment: bioactive herbal compounds, polymer delivery systems, and computational bioprospecting of functional targets.Pharmacological reports : PR · 2026Review
- Spectrochemical, medicinal, and toxicological studies of moxifloxacin and its novel analogs: a quantum chemistry and drug discovery approach.RSC advances · 2026Article
- Novel Pyrazoline Derivatives as Therapeutic Candidate for Alzheimer's Disease: An Integrated Network Pharmacology and 3D-QSAR Modelling.Bioinformatics and biology insights · 2026Article
- In silico approaches unveil the mechanism of action of Eclipta prostrata against acute myeloid leukemia.Scientific reports · 2025Article
- Investigating the unbinding mechanisms and kinetics of MmpL3 inhibitors: A computational study.Protein science : a publication of the Protein Society · 2025Article
- The physics-AI dialogue in drug design.RSC medicinal chemistry · 2025Review
- Stereo-selectivity of enantiomeric inhibitors to ubiquitin-specific protease 7 (USP7) dissected by molecular docking, molecular dynamics simulations, and binding free energy calculations.Molecular diversity · 2025Article
- Multi-Objective Loss Function For Free Energy Calculations.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2025Article
- Article
- Computational identification and analysis of CNP0269688 as a natural product inhibitor disrupting the interaction between the HIV matrix domain and tRNA.Frontiers in chemistry · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
introductionFor rational drug design, it is crucial to understand the receptor-drug binding processes and mechanisms. A new era for the use of computer simulations in predicting drug-receptor interactions at an atomic level has begun with remarkable advances in supercomputing and methodological breakthroughs. AREAS COVERED: End-point free energy calculation methods such as Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) or Molecular-Mechanics/Generalized Born Surface Area (MM/GBSA), free energy perturbation (FEP), and thermodynamic integration (TI) are commonly used for binding free energy calculations in drug discovery. In addition, kinetic dissociation and association rate constants ( EXPERT OPINION: The applications of computational methods in drug discovery and design are expanding, thanks to improved predictions of the binding free energy and kinetic rates of drug molecules. Recent microsecond-timescale enhanced sampling simulations have made it possible to accurately capture repetitive ligand binding and dissociation, facilitating more efficient and accurate calculations of ligand binding free energy and kinetics.
Indexed as
Identifiers
What Socratic 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 Socratic graph.