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ARCTIC-3D: all you want to know about protein-specific interfaces

ARCTIC-3D is a software for data-mining and clustering of protein interface information. It allows you to retrieve all the existing interface information for your desired protein from the PDBE graph database, grouping similar interfaces in interacting surfaces.

The software first checks your input (a uniprot ID, a FASTA file, or a PDB file), and then retrieves the existing interaction data from the graph API. Such interfaces are projected on a selected PDB structure and their dissimilarity is calculated, thus allowing for the application of a hierarchical clustering algorithm.

In output you will see how your favourite protein can display different binding surfaces, each one characterised by few residues that are always present (hotspots) and other amino acids which are at the interface only from time to time.

input interface file
Set of comma-separated partner IDs to exclude from the search
Set of comma-separated PDB IDs to exclude from the search
PDBid to be used
Chain to be used
Threshold for interface clustering
Linkage strategy to be used
fraction of interface residues to be present in a PDB structure
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This work is co-funded by the Horizon 2020 projects EOSC-hub and EGI-ACE (grant numbers 777536 and 101017567), BioExcel (grant numbers 823830 and 675728)
and by a computing grant from NWO-ENW (project number 2019.053).