Dear community, We are excited to announce that the RCSB Protein Data Bank has recently introduced a new feature that allows you to define searches by uploading your own experimental data files or Computed Structure Models.
This feature is particularly useful for those working with AlphaFold2 or ESMfold predictions, homology models, molecular dynamic trajectories, and previously unpublished structures. Various file formats such as .cif, .pdb, .ent, and gzipped (.gz) files are supported, enabling you to quickly and easily analyze your data and screen the whole PDB archive for structural similarity. Searching in 1 million Computed Structure Models from AlphaFold DB and ModelArchive is available as well. By switching to the "File Upload" mode in the Advanced Search Structure Similarity <https://www.rcsb.org/search/advanced/structure> and Structure Motif <https://www.rcsb.org/search/advanced/strucmotif> options, you can use RCSB.org's novel method to detect similarity between protein shapes of any size. The system assesses global 3D-shape similarity using BioZernike descriptors, enabling you to find structures whose volumes are globally similar to your query structure. The Structural Motif option is also available, which allows you to search for structures containing specific amino acids in a characteristic local arrangement. This feature is particularly useful for gaining insights into protein function and evolution by searching for active or ligand binding sites. Queries can be conveniently defined using RCSB.org’s Mol* 3D Viewer. To access these features, simply upload your data and start exploring. The search results are accessible through a unique URL for 90 days, allowing you to share and bookmark your findings with colleagues. For more detailed instructions, please refer to the user guide documentation available on RCSB.org (https://www.rcsb.org/docs/search-and-browse/advanced-search/structure-similarity-search#query-for-structures-not-available-from-rcsborg and https://www.rcsb.org/docs/search-and-browse/advanced-search/structure-motif-search#uploading-your-own-local-file). We hope this new feature will be valuable to your research and we look forward to seeing the scientific discoveries that come from it. Kind regards, Sebastian Bittrich ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
