ArticleScientific reports2016
QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 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
118 citing papers in PubMed.
- Single-Molecule Force Spectroscopy: Experiments, Analysis, and Simulations.Methods in molecular biology (Clifton, N.J.) · 2027Article
- The urinary pathobiont Actinobaculum massiliense can generate androgens via the dirAB pathway.Nature communications · 2026Article
- Mapping of dynamic allostery within p38 alpha kinase via network analyses and NMR spectroscopy.Nature communications · 2026Article
- Article
- E50A Mutation Increases the Bioluminescence Activity of picALuc.Biosensors · 2026Article
- Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress.Science advances · 2026Article
- Cadherin-23 mutations cause calcium-dependent, allele-sensitive mechanosensory defects.iScience · 2026Article
- The translation factor eIF4E is a key mediator of doxorubicin resistance: insights from a triple-negative breast cancer model.Scientific reports · 2026Article
- Deciphering Pharmacological Targets of Plumbagin in Cisplatin-resistant Ovarian Cancer Model usingCurrent pharmaceutical design · 2026Article
- Characterization and modulation of human insulin degrading enzyme conformational dynamics to control enzyme activity.bioRxiv : the preprint server for biology · 2025Article
- Molecular simulations meet personalized medicine: The mechanism of action of CLC-5 antiporter and the origin of Dent's disease.PNAS nexus · 2025Article
- First In Silico Study of TwoInternational journal of molecular sciences · 2025Article
- Structure-Based Insights into Stefin-Mediated Targeting of Fowlerpain-1: Towards Novel Therapeutics forPharmaceuticals (Basel, Switzerland) · 2025Article
- Sparstolonin B attenuates MRSA-induced wound and peritonitis infection: in vivo, phytochemical, and computational investigation.Scientific reports · 2025Article
- DynamiSpectra: A Python Software Package and Web Platform for Molecular Dynamics Data Analysis in Computational Biology.Journal of chemical information and modeling · 2025Article
- UltrastrongScience advances · 2025Article
- Multi-state catch bond formed in the Izumo1:Juno complex that initiates human fertilization.Nature communications · 2025Article
- 4D structural biology-quantitative dynamics in the eukaryotic RNA exosome complex.Nature communications · 2025Article
- Pedagogical applications of all-atom molecular dynamics simulation in coal seam seepage mechanics.Scientific reports · 2025Article
- Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody-Protein Complexes.Proteins · 2025Article
58 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
7 authors.
Funding
Abstract
The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services.
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.