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Updated: Jun 13, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Dynameomics: a comprehensive database of protein dynamics.
Marc W van der Kamp1, R Dustin Schaeffer, Amanda L Jonsson
1Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA.
Structure (London, England : 1993)
|April 20, 2010
Summary
This study presents a large database of protein dynamics simulations, offering insights into protein folding and function. The data enables mining for applications in structure building, genetic variation impact, and drug design.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Protein dynamics are crucial for understanding protein function and folding mechanisms.
- A comprehensive understanding of protein behavior requires extensive simulation data.
Purpose of the Study:
- To create and describe a large-scale database of molecular dynamics simulations for protein native states and unfolding pathways.
- To demonstrate the utility of this database for extracting information relevant to protein folding, structure, genetics, and drug design.
Main Methods:
- Performed over 11,000 molecular dynamics simulations across 2000+ protein/peptide systems.
- Developed an innovative database to store and organize simulation data.
- Mined the database for specific applications and analyses.
Main Results:
- The database contains extensive data on protein dynamics and folding/unfolding pathways for a majority of globular protein folds.
- Examples show successful data mining for protein folding, structure prediction, SNP effects, and drug design.
- Public access is provided for native state simulations and analyses of 100 metafolds.
Conclusions:
- The Dynameomics database provides a valuable resource for studying protein dynamics and folding.
- The data facilitates diverse research areas, including structural biology, bioinformatics, and therapeutic development.
- Publicly accessible data promotes further research and discovery in protein science.
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