ArticleInternational journal of molecular sciences2025
Unveiling Dynamic Hotspots in Protein-Ligand Binding: Accelerating Target and Drug Discovery Approaches.
Article in International journal of molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Exploring the Neuropharmacological Potential of Ligustrum sinense Relevant to Parkinson's Disease: In Vivo and In Silico Study.Chemistry & biodiversity · 2026Article
- Reimagining antimicrobial resistance: AI-driven predictive epidemiology and the C-AMRE framework for next-generation antibiotic discovery.The Journal of antibiotics · 2026Review
- Mutant-Selective Binding ofInternational journal of molecular sciences · 2026Article
- Integrated network pharmacology reveal new key curcumin-binding targets in triple-negative breast cancer.Discover oncology · 2026Article
- Comprehensive metabolomic profiling of Egyptian Salvia species reveals promising leads for chemopreventive and anti-inflammatory drug development: In vitro and In silico study.Scientific reports · 2026Article
- Bioinformatics and computational exploration of novel inhibitors targeting KRAS G12C mutant protein in lung adenocarcinoma.Discover oncology · 2026Article
- Integrated Bioinformatics Analysis and In Vitro Evidence Support HSP90AA1 as a Candidate Target ofInternational journal of molecular sciences · 2026Article
- Computational renaissance in herbal medicine: A 20-year bibliometric deciphering of molecular dynamics simulations reshaping traditional Chinese medicine drug discovery.Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society · 2026Article
- Synthesis, Biological Evaluation, and Computational Studies of PhenolicMarine drugs · 2026Article
- A Machine Learning-Guided Approach for Identifying Potential HCAR1 Antagonists in Lactate-Driven Cancers.ACS omega · 2026Article
- Exploring and validating the molecular targets and potential mechanisms of shikonin against osteomyelitis through computational analyses and animal experiments.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- In-Silico Exploration of the StreptomeDB Database for Potential Irreversible DprE1 Inhibitors toward Antitubercular Treatment.ChemistryOpen · 2025Article
- Strategies for the drug development of cancer therapeutics.Frontiers in pharmacology · 2025Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computational methods have transformed target and drug discovery, significantly accelerating the identification of biological targets and lead compounds. Despite its limitations, in silico molecular docking represents a foundational tool. Molecular Dynamics (MD) simulations, employing accurate force fields, provide near-realistic insights into a compound's behavior within a biological target. However, docking and MD predictions may be unreliable without precise knowledge of the target binding site. Through MD simulations, we investigated 100 co-crystal structures of biological targets complexed with active compounds, identifying key structural and energy dynamic features that govern target-ligand interactions. Our analysis provides a detailed quantitative description of these parameters, offering critical validation for improving the predictive reliability of docking and MD simulations. This work provides a robust framework for refining early-stage drug discovery and target identification.
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