Related Experiment Video
Updated: Jul 2, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
A dataset of small protein conformational ensembles from all-atom molecular dynamics simulations
Ying Hu1,2, Xin Yang1,2, Xinlei Zhu1,2
1School of Information Science and Technology & AI for Science Center, Northeast Normal University, Changchun, 130117, China.
Abstract:
Small proteins, with more pronounced conformational flexibility, are crucial in biological processes and their function is linked to their high flexibility. While several databases are widely used to characterize protein dynamics, a significant data gap remains for small proteins comprising 5-100 amino acids. To address this, we present DynoDB, a dataset of small protein conformational ensembles from all-atom molecular dynamics simulations. In DynoDB, a total of 8,385 small proteins were subjected to all-atom molecular dynamics simulations of 100 ns each. We generated about 9.1 TB of trajectory data, covering diverse functional types of biomolecules, along with structural and functional annotations, as well as dynamic analysis results. This dataset systematically captures the conformational dynamics of the small proteins, serving as a dedicated data resource for the field of peptide design, vaccine development, antimicrobial screening, and AI modeling.
Related Concept Videos
Protein Organization
The primary structure of a protein is its amino acid sequence.
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Families
Intrinsically Disordered Proteins
Globular and Fibrous Proteins
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
