AlphaFind — discover structure similarity across the proteome in AlphaFold DB

• Authors: SLANINÁKOVÁ Terézia; PROCHÁZKA David; OĽHA Jaroslav; ROŠINEC Adrián; GREŠOVÁ Katarína; ČILLÍK Jakub; JÁNOŠOVÁ Miriama; PORUBSKÁ Jana; SVOBODOVÁ Radka; DOHNAL Vlastislav; ANTOL Matej
• Year of publication: 2024
• Type: Conference abstract
• Description: AlphaFind is a web-based search engine that allows for structure-based search of the entire AFDB. Uniprot ID, PDB ID, or Gene Symbol is accepted as input – AlphaFind will return the most similar proteins found within AlphaFold DB, with an option to perform additional search to extend and refine the results. The search results are grouped by their source organism and displayed along with their TM-Score and RMSD measures (relative to the query protein). If the result proteins are experimentally found, we provide all associated PDB IDs. The 3D visualizations of the structural overlap of the proteins are provided using NGL Viewer, and the additional filters at the top of the results table can be used to find specific organisms or Uniprot IDs.

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