ArticleStructure (London, England : 1993)2010
Dynameomics: a comprehensive database of protein dynamics.
Article in Structure (London, England : 1993), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 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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Who cites it
76 citing papers in PubMed, 158 citations in OpenAlex.
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Fast prediction of protein flexibility.Bioinformatics (Oxford, England) · 2026Article
- DynaRepo: the repository of macromolecular conformational dynamics.Nucleic acids research · 2026Article
- A FAIR-Compliant Management Solution for Molecular Simulation Trajectories.Journal of chemical information and modeling · 2025Article
- Layer-By-Layer Functionalized Gauze With Designed α-Sheet Peptides Inhibits E. coli and S. aureus Biofilm Formation.Journal of biomedical materials research. Part A · 2025Article
- Article
- mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics.Scientific data · 2024Article
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- Designed De Novo α-Sheet Peptides Destabilize Bacterial Biofilms and Increase the Susceptibility ofInternational journal of molecular sciences · 2024Article
- ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures.Database : the journal of biological databases and curation · 2024Article
- A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort.Nucleic acids research · 2024Article
- ATLAS: protein flexibility description from atomistic molecular dynamics simulations.Nucleic acids research · 2024Article
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- Building protein structure-specific rotamer libraries.Bioinformatics (Oxford, England) · 2023Article
- Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles.Computational and structural biotechnology journal · 2023Article
- The role of α-sheet structure in amyloidogenesis: characterization and implications.Open biology · 2022Review
- High Energy Channeling and Malleable Transition States: Molecular Dynamics Simulations and Free Energy Landscapes for the Thermal Unfolding of Protein U1A and 13 Mutants.Biomolecules · 2022Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- Towards the Idea of Molecular Brains.International journal of molecular sciences · 2021Review
- Data-driven network models for genetic circuits from time-series data with incomplete measurements.Journal of the Royal Society, Interface · 2021Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
Abstract
The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 2000 protein/peptide systems (approximately 11,000 independent simulations) representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through http://www.dynameomics.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.