ArticleInternational journal of molecular sciences2023
MD-Ligand-Receptor: A High-Performance Computing Tool for Characterizing Ligand-Receptor Binding Interactions in Molecular Dynamics Trajectories.
Article in International journal of molecular sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- Integrated Computer-Aided Drug Design: Advances in GPCR Natural Ligand Discovery.Cell biochemistry and biophysics · 2026Review
- Pharmacokinetics, molecular docking, and molecular dynamics simulation unveil novel lichen-derived scaffolds targeting PBP2a MRSA.Frontiers in bioinformatics · 2026Article
- Natural Fatty Acids as Dual ACE2-Inflammatory Modulators: Integrated Computational Framework for Pandemic Preparedness.International journal of molecular sciences · 2025Article
- Modulation of Aging Diseases via RAGE Targets: A Dietary Intervention Review.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Lignin-Derived Oligomers as Promising mTOR Inhibitors: Insights from Dynamics Simulations.International journal of molecular sciences · 2025Article
- HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.BMC bioinformatics · 2025Article
- Exploring novel and potent glycogen synthase kinase-3β inhibitors through systematic drug designing approach.Scientific reports · 2025Article
- An insight for the inhibition of anxiolytic and anti-convulsant effects in zebrafish using the curcumins via exploring molecular docking and molecular dynamics simulations.Molecular diversity · 2025Article
- Structure-based molecular screening and dynamic simulation of phytocompounds targeting VEGFR-2: a novel therapeutic approach for papillary thyroid carcinoma.Frontiers in pharmacology · 2025Article
- Decoding the structural and functional diversity of GABAFrontiers in pharmacology · 2025Review
- Small molecule modulation of protein corona for deep plasma proteome profiling.Nature communications · 2024Article
- Phytoconstituents of Withania somnifera (L.) Dunal (Ashwagandha) unveiled potential cerebroside sulfotransferase inhibitors: insight through virtual screening, molecular dynamics, toxicity, and reverse pharmacophore analysis.Journal of biological engineering · 2024Article
- Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules.bioRxiv : the preprint server for biology · 2024Article
- HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation.BMC bioinformatics · 2024Article
- Article
- Green and Efficient Extraction of Phenolic Components from Plants with Supramolecular Solvents: Experimental and Theoretical Studies.Molecules (Basel, Switzerland) · 2024Article
- Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics simulation is a widely employed computational technique for studying the dynamic behavior of molecular systems over time. By simulating macromolecular biological systems consisting of a drug, a receptor and a solvated environment with thousands of water molecules, MD allows for realistic ligand-receptor binding interactions (lrbi) to be studied. In this study, we present MD-ligand-receptor (MDLR), a state-of-the-art software designed to explore the intricate interactions between ligands and receptors over time using molecular dynamics trajectories. Unlike traditional static analysis tools, MDLR goes beyond simply taking a snapshot of ligand-receptor binding interactions (lrbi), uncovering long-lasting molecular interactions and predicting the time-dependent inhibitory activity of specific drugs. With MDLR, researchers can gain insights into the dynamic behavior of complex ligand-receptor systems. Our pipeline is optimized for high-performance computing, capable of efficiently processing vast molecular dynamics trajectories on multicore Linux servers or even multinode HPC clusters. In the latter case, MDLR allows the user to analyze large trajectories in a very short time. To facilitate the exploration and visualization of lrbi, we provide an intuitive Python notebook (Jupyter), which allows users to examine and interpret the results through various graphical representations.
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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.