| URL: | https://cfold.bme.uic.edu/castpfold |
| Full name: | Computed Atlas of Surface Topography of the universe of protein Folds |
| Description: | The CASTpFold database enhances the original CASTp by incorporating AlphaFold2-predicted protein structures, expanding its repository to include over 183 million protein structures. It offers detailed analysis of protein topographies, such as surface pockets, cavities, and channels, and integrates functional annotations with Gene Ontology and Enzyme Commission numbers. |
| Year founded: | 2024 |
| Last update: | 2024-05-23 |
| Version: | v1.0 |
| Accessibility: |
Accessible
|
| Country/Region: | United States |
| Data type: | |
| Data object: |
NA
|
| Database category: | |
| Major species: |
NA
|
| Keywords: |
| University/Institution: | University of Illinois at Chicago |
| Address: | Chicago, IL 60612, USA |
| City: | Chicago |
| Province/State: | |
| Country/Region: | United States |
| Contact name (PI/Team): | Jie Liang |
| Contact email (PI/Helpdesk): | jliang@uic.edu |
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CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds. [PMID: 38783102]
Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a widely used web server for locating, delineating, and measuring these geometric and topological properties of protein structures. Recent developments in AI-based protein structure prediction such as AlphaFold2 (AF2) have significantly expanded our knowledge on protein structures. Here we present CASTpFold, a continuation of CASTp that provides accurate and comprehensive identifications and quantifications of protein topography. It now provides (i) results on an expanded database of proteins, including the Protein Data Bank (PDB) and non-singleton representative structures of AlphaFold2 structures, covering 183 million AF2 structures; (ii) functional pockets prediction with corresponding Gene Ontology (GO) terms or Enzyme Commission (EC) numbers for AF2-predicted structures and (iii) pocket similarity search function for surface and protein-protein interface pockets. The CASTpFold web server is freely accessible at https://cfold.bme.uic.edu/castpfold/. |
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CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds. [PMID: 38766001]
Geometric and topological properties of protein structures, including surface pockets, interior cavities, and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a widely used web server for locating, delineating, and measuring these geometric and topological properties of protein structures. Recent developments in AI-based protein structure prediction such as AlphaFold2 (AF2) have significantly expanded our knowledge on protein structures. Here we present CASTpFold, a continuation of CASTp that provides accurate and comprehensive identifications and quantifications of protein topography. It now provides (i) results on an expanded database of proteins, including the Protein Data Bank (PDB) and non-singleton representative structures of AlphaFold2 structures, covering 183 million AF2 structures; (ii) functional pockets prediction with corresponding Gene Ontology (GO) terms or Enzyme Commission (EC) numbers for AF2-predicted structures; and (iii) pocket similarity search function for surface and protein-protein interface pockets. The CASTpFold web server is freely accessible at https://cfold.bme.uic.edu/castpfold/. |