ArticleBioinformatics (Oxford, England)2011
ProDy: protein dynamics inferred from theory and experiments.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 594 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
594 citing papers in PubMed.
- Assessing the Generalizability of Machine Learning and Physics-Based Methods with DNA-Encoded Libraries.Journal of chemical information and modeling · 2026Article
- Cancer treatment alters mutant selection in normal esophagus.Nature genetics · 2026Article
- A Minimalist Model for Navigating Conformational Landscape Uncovers the Activation Mechanism of βACS physical chemistry Au · 2026Article
- Surface dielectric barrier discharge plasma priming enhances salt-tolerant wheat germination through predicted AMY1.1 redox stabilization.Scientific reports · 2026Article
- Diacerein Protects Against Obesity-Related Cardiovascular Injury: Evidence from In Silico and In Vivo Studies.Applied biochemistry and biotechnology · 2026Article
- RinPy, a Python Package for Residue Interaction Network Model to Analyze Protein Structures and Predict Ligand Binding Sites.Journal of chemical information and modeling · 2026Article
- Structure-based computational investigation of potential TarA inhibitors in Staphylococcus aureus.Molecular diversity · 2026Article
- Structural basis of Mlc-mediated transcriptional regulation of carbohydrate metabolism.Nature communications · 2026Article
- Article
- Multiply Perturbed Response: A Computational Protocol to Identify Cooperative Allosteric Residue Combinations Driving Protein Conformational Transitions.Bio-protocol · 2026Article
- Elliptical β-barrel deformation underlies gating in VDAC1.Protein science : a publication of the Protein Society · 2026Article
- Integrated in silico and in vitro assessment of Azadirachta indica leaf extract against multi-drug resistant Citrobacter koseri and Staphylococcus saprophyticus.Scientific reports · 2026Article
- Functional Calmodulin States Are Selected from an Electrostatically Tuned Free Energy Landscape.Journal of chemical information and modeling · 2026Article
- Introduction of regioselective bacterial heme oxygenases into Arabidopsis hy1-1 supports the retrograde heme signaling hypothesis.Plant physiology · 2026Article
- ERK autoinhibition mechanism informs a drug combination strategy.Protein science : a publication of the Protein Society · 2026Article
- Structuring Disorder via Supervised Molecular Dynamics: Uncovering Arginine-Glycine-Glycine-Mediated Ribonucleic Acid-Intrinsically Disordered Region Recognition Mechanisms.Journal of chemical information and modeling · 2026Article
- Assessing the Generalizability of Machine Learning and Physics-Based Methods with DNA-Encoded Libraries.bioRxiv : the preprint server for biology · 2026Article
- Free Energy and Flexibility Analysis of Autoinhibited Human BRAF.Journal of chemical information and modeling · 2026Article
- Linking the kinetic mechanism to structural dynamics required for nucleotide hydrolysis by an alphavirus nsP2 RNA helicase.bioRxiv : the preprint server for biology · 2026Article
- Graph neural networks can predict ketosynthase substrate specificity.Scientific reports · 2026Article
534 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
3 authors.
Funding
Abstract
summaryWe developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. Numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. ProDy application programming interface (API) has been designed so that users can easily extend the software and implement new methods. AVAILABILITY: ProDy is open source and freely available under GNU General Public License from http://www.csb.pitt.edu/ProDy/.
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.