ReviewAdvances and applications in bioinformatics and chemistry : AABC2015
Molecular dynamics simulations: advances and applications.
Review in Advances and applications in bioinformatics and chemistry : AABC, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 356 papers.
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Who cites it
356 citing papers in PubMed.
- Binding of Anthracyclines Within DNA-Topoisomerase ΙΙ Cleavage Complexes: Thermodynamics and Interactions.Journal of chemical information and modeling · 2026Article
- Multiscale modeling primer: Focus on chromatin and epigenetics.The Journal of biological chemistry · 2026Review
- Antimicrobial peptides as computational candidates for SARS-CoV-2 papain-like protease inhibition.Scientific reports · 2026Article
- Identification of Potential SARS-CoV-2 Main Protease (MPro) Inhibitors Through Pharmacophore Modeling, Molecular Docking, and Molecular Dynamics Simulation Approaches.International journal of molecular sciences · 2026Article
- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- POMsDB: a QM derived molecular properties and parameters database for Polyoxometalates.Scientific data · 2026Article
- Tutorial for Atomistic and Coarse-Grained Simulations of Membrane-Nanoplastic Interactions Using GROMACS.The journal of physical chemistry. B · 2026Article
- A multi-dimensional engineering strategy integrating computational design, self-cyclization and whole cell biocatalysis for efficient epilactose production.Food chemistry: X · 2026Article
- Synthesis, Biological Evaluation, Molecular Docking and Molecular Dynamics of Substituted Thieno[2,3-d]pyrimidine Derivatives as Potential Anti-Alzheimer Agents.International journal of molecular sciences · 2026Article
- Computational Investigation of GNMT-Catalyzed Methyl Transfer Reaction: Integrating MD, QM, and ML Approaches.Journal of computational chemistry · 2026Article
- Molecular Dynamics Analysis of the Stereoselective Recognition of Myo-Inositol and D-Chiro-Inositol in a Protein-Based Biosensor.Sensors (Basel, Switzerland) · 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
- Antiviral Activity of Polyene Macrolides Against Newcastle Disease Virus: Computational and Experimental Insights.Molecules (Basel, Switzerland) · 2026Article
- Structural bioinformatics insights into UDP-galactopyranose mutase (UGM) as a novel drug target for antifilarial therapy against human filarial parasite Brugia malayi.Molecular diversity · 2026Article
- Streptococcus-derived CpsA-CpsC fusion protein induces apoptosis in cervical cancer cells through in silico and in vitro methods.Scientific reports · 2026Article
- Design, synthesis, and anticancer evaluation of novel pyrrole-pyrazoline/chalcone hybrids:RSC medicinal chemistry · 2026Article
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
- Comparative insecticidal efficacy and biochemical impact of nano-encapsulated citronella and geranium essential oils against Spodoptera littoralis (Lepidoptera: Noctuidae).Scientific reports · 2026Article
- Click chemistry of phenyl 1,2,3-triazole-2-pyridylpiperazine hybrids: synthesis, targeted anticancer activity, molecular modeling and computational studies.RSC advances · 2026Article
- Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026Review
296 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
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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.