AlphaKnot 2.0 – database and server to measure entanglement in AlphaFold-solved protein models while considering pLDDT confidence values. AlphaKnot 2.0 has two main functions: 1) providing researchers with a webserver for analyzing knotting in their own AlphaFold predictions and 2) cataloging knotting in AlphaFold (v4 and v1) predictions of over 200M proteins for which models have been published. Cataloged structures are compared with ESMFold predictions. New advanced search and API will help you to collect precisely these data which you need!
The topology is defined in a probabilistic way. The dominant knot type as well as the computed locations of the knot cores (i.e. minimal portions of protein backbones that form a given knot type) are shown for each protein structure.
Input file should be in the standard CIF file format (https://en.wikipedia.org/wiki/Crystallographic_Information_File).
Input file should be in the standard PDB file format (http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html).
Up to 10 files in CIF, CIF.gz or PDB format can be uploaded at once. These can be different models of the same structure (as in this example) or any other set of structures.