ArticlePLoS computational biology2025
mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data.
Article in PLoS computational biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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.
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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.
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Who cites it
21 citing papers in PubMed.
- Uncoupling of the allosteric signalling network in the βNature communications · 2026Article
- Nano-GAngewandte Chemie (International ed. in English) · 2026Article
- Role of Ambler Position 104 in Defining Substrate Specificity in the KPC Family of β-Lactamases.ACS infectious diseases · 2026Article
- Molecular Dynamics Insights intoInternational journal of molecular sciences · 2026Article
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- Conformational Signatures of Preassembled and Active Complexes of 5-HTJournal of chemical information and modeling · 2025Article
- A Novel Multi-Tiered Hybrid Virtual Screening Pipeline for the Discovery of WDR5-MLL1 Interaction Disruptors in Precision Cancer Therapy.ACS omega · 2025Article
- A Mutation-Based Reverse Vaccinology Approach Considering Variability in Epitopes to Combat Multi-Strains: A Study Using Glycoprotein of LASV.Journal of cellular and molecular medicine · 2025Article
- Computational Analysis ofACS chemical neuroscience · 2025Article
- Transient ligand contacts of the intrinsically disordered N-terminus of neuropeptide YNature communications · 2025Article
- DynamiSpectra: A Python Software Package and Web Platform for Molecular Dynamics Data Analysis in Computational Biology.Journal of chemical information and modeling · 2025Article
- In silico exploration of anticancer plant phytochemicals for EGFR-targeted lung cancer therapy.Scientific reports · 2025Article
- Structural Insights into the Substrate Egress Pathways Explains Specificity and Inhibition of Human Glucose Transporters (GLUT1 and GLUT9).ACS pharmacology & translational science · 2025Article
- Ligand and Residue Free Energy Perturbations Solve the Dual Binding Mode Proposal for an AThe journal of physical chemistry. B · 2025Article
- Generic residue numbering of the GAIN domain of adhesion GPCRs.Nature communications · 2025Article
- Cutting-edge Bioinformatics strategies for synthesizing Cyclotriazadisulfonamide (CADA) analogs in next-Generation HIV therapies.Scientific reports · 2024Article
- Mechanistic insights into G-protein coupling with an agonist-bound G-protein-coupled receptor.Nature structural & molecular biology · 2024Article
- Article
- MUTATIONEXPLORER- A WEBSERVER FOR MUTATION OF PROTEINS AND 3D VISUALIZATION OF ENERGETIC IMPACTS.bioRxiv : the preprint server for biology · 2024Article
- Structural Characteristics of PON1 with Leu55Met and Gln192Arg Variants Influencing Oxidative-Stress-Related Diseases: An Integrated Molecular Modeling and Dynamics Study.Medicina (Kaunas, Lithuania) · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We present mdciao, an open-source command line tool and Python Application-Programming-Interface (API) for easy, one-shot analysis and representation of molecular dynamics (MD) simulation data. Building upon the widely used concept of residue-residue contact-frequencies, mdciao offers a wide spectrum of further analysis and representations, enriched with available domain specific annotations. The user-friendly interface offers pre-packaged solutions for non-expert users, while keeping customizability for expert ones. Emphasis has been put into automatically producing annotated, production-ready figures and tables. Furthermore, seamless on-the-fly query and inclusion of domain-specific generic residue numbering for GPCRs, GAIN-domains, G-proteins, and kinases is made possible through online lookups. This allows for easy selection and comparison across different systems, regardless of sequence identity, target residues or domains. Finally, the fully documented Python API allows users to include the basic or advanced mdciao functions in their analysis workflows, and provides numerous examples and Jupyter Notebook Tutorials. The source code is published under the GNU Lesser General Public License v3.0 or later and hosted on https://github.com/gph82/mdciao, and the documentation, including guides and examples, can be found at https://www.mdciao.org.
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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.