ArticleCurrent protocols in bioinformatics2008
Using VMD: an introductory tutorial.
Article in Current protocols in bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 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
80 citing papers in PubMed.
- From wireframes to immersive reality: a historical perspective on molecular visualization software.Briefings in bioinformatics · 2026Review
- In-plane thermal transport and interfacial thermal resistance in carbon/silicon carbide van der Waals heteronanotubes: a molecular dynamics study.RSC advances · 2026Article
- Eco-Friendly Synthesis, Physicochemical Characterization, and In Vitro Biological Evaluation of Plant-Derived Bioactive-Loaded Chitosan Nanoparticles Supported by Molecular Modeling Studies.Molecules (Basel, Switzerland) · 2026Article
- Beyond chemical composition: solvent pretreatment modulates supramolecular assembly and interactions with MRSA to enhance antibacterial efficacy of Scutellariae Radix-Coptidis Rhizoma.Chinese medicine · 2026Article
- Tuning the thermal decomposition pathways and sensitivity of 1,2,3-triazole-based energetic regioisomers via external electric fields: a dft mechanism study.Journal of molecular modeling · 2026Article
- Structural Basis for TGF-β Mimetic Peptide-Induced Signaling Activation Through Molecular Dynamics Simulations.International journal of molecular sciences · 2025Article
- Hydrophobicity-Driven Disruption Mechanism in Kindlin-3 Induced by Leukocyte Adhesion Deficiency Mutation.ACS omega · 2025Article
- Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.Nature communications · 2025Article
- Molecular mechanisms and computational insights into human SGLTs: advancing toward selective SGLT1 inhibition.Frontiers in molecular biosciences · 2025Review
- Fc-FcγRI Complexes: Molecular Dynamics Simulations Shed Light on Ectodomain D3's Potential Role in IgG Binding.ACS omega · 2024Article
- Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?Protein science : a publication of the Protein Society · 2024Article
- Identification of a Clade-Specific HLA-C*03:02 CTL Epitope GY9 Derived from the HIV-1 p17 Matrix Protein.International journal of molecular sciences · 2024Article
- Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.Research square · 2024Article
- Reconnaissance of Allostery via the Restoration of Native p53 DNA-Binding Domain Dynamics in Y220C Mutant p53 Tumor Suppressor Protein.ACS omega · 2024Article
- Identification and Characterization of the Very-Low-Density Lipoprotein Receptor Gene fromAnimals : an open access journal from MDPI · 2023Article
- Structural Basis of the Binding Mode of the Antineoplastic Compound Motixafortide (BL-8040) in the CXCR4 Chemokine Receptor.International journal of molecular sciences · 2023Article
- In Silico Screening of Drugs That Target Different Forms of E Protein for Potential Treatment of COVID-19.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Clustering molecular dynamics conformations of the CC'-loop of the PD-1 immuno-checkpoint receptor.Computational and structural biotechnology journal · 2023Article
- Variable Regions of p53 Isoforms Allosterically Hard Code DNA Interaction.The journal of physical chemistry. B · 2022Article
- Mutagenic Activation of Glutathione Peroxidase-4: Approaches toward Rational Design of Allosteric Drugs.ACS omega · 2022Article
20 more citing papers are in PubMed but not listed here.
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
VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. This unit will serve as an introductory VMD tutorial. We will present several step-by-step examples of some of VMD's most popular features, including visualizing molecules in three dimensions with different drawing and coloring methods, rendering publication-quality figures, animating and analyzing the trajectory of a molecular dynamics simulation, scripting in the text-based Tcl/Tk interface, and analyzing both sequence and structure data for proteins.
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.