FoldSeek
FoldSeek is a computational tool for comparing and aligning protein structures. It efficiently identifies similar 3D conformations across different protein families, helping to understand evolutionary relationships and predict protein function. This tool is valuable for drug design and studying protein dynamics in structural biology.
Find others like 3kwd
Inputs for Structural Comparison
- PDB file: 3D structures of the proteins to be compared, provided in PDB format.
- Query Structure: The specific protein structure you want to use as a reference for comparison.
- Database of Structures: A set of PDB files that contains the protein structures to be searched for similarities.
Outputs from FoldSeek
- List of Hits: A list of database hits that are structurally aligned to the input protein.
- TM-Score: A score indicating structural identity between two proteins, ranging from 0.0 (no match) to 1.0 (exact match), with 0.5 indicating similar folds or families.
- Fident: The percentage of sequence identity between the database hit and the input protein after structural alignment, where 100 indicates an identical sequence match.
Runtime
Scales with the size of the database used. Typically 0.5 to 1.0 min.
Examples of FoldSeek Applications
Find similar proteins to MA998
Lookup structures like P42212
