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Web server manual

ARCTIC-3D

The ARCTIC-3D web server at https://wenmr.science.uu.nl/arctic3d retrieves all the interfaces of a protein that are known from experimental structures and clusters them into binding surfaces. You need an account on the portal to submit a job.

How ARCTIC-3D works

  1. ARCTIC-3D retrieves the interfaces of your protein with its partners (proteins, and optionally ligands) from the PDBe graph API.
  2. It projects them on one structure of your protein: by default the PDB structure that contains the most interface residues.
  3. It computes the dissimilarity of every pair of interfaces and clusters the interfaces hierarchically: interfaces that overlap on the surface of the protein form one binding surface.
  4. For each binding surface, it gives the probability of each residue, the fraction of the interfaces of that surface it is part of.

Input

UniProt ID

The UniProt accession of your protein (for example P68871). If you do not know it, search UniProt for the name of your protein: for Hemoglobin, the first result is Hemoglobin subunit beta, with the accession (Entry) P68871.

Entering the UniProt ID is enough to submit a job; the other parameters are optional.

Interface parameters

  • Uniprot IDs to be excluded: partners whose interfaces should not be considered, comma-separated. For example P68871 excludes the homodimer interfaces of P68871.
  • PDB IDs to be excluded: PDB entries to leave out of the search, comma-separated (for example 7pcq,5jdo): because you do not trust an interface, or to leave it out for benchmarking.
  • Interface coverage cutoff (default 0.7): the fraction of the residues of an interface that must be present in the structure for the interface to be kept. With 0.5, at least half of the residues of every interface must be in the structure.

Structure parameters

  • PDB ID to be used: the PDB entry to project the interfaces on, instead of the one with the most interface residues (for example 1dxt).
  • Chain ID to be used: the chain of that entry (for example B).

Clustering parameters

The interfaces are clustered with a hierarchical clustering.

  • Threshold (default 0.866, an angle of 60°): where the hierarchy is cut, below 1. A lower threshold gives a stricter clustering and more binding surfaces; a higher threshold gives fewer, more heterogeneous surfaces.
  • Linkage strategy (default average): how the distance between two clusters is computed. With average, it is the average distance between their interfaces.
  • Minimum number of residues in clusters (default 0): binding surfaces of one or two residues carry little biological meaning. With 3, surfaces of fewer than three residues are discarded.

Clustering the partners

The partners of your protein can also be clustered by their QuickGO annotations: subcellular location, protein function and biological process. Select one or more of the three.

Output

Report

The results page shows the ARCTIC-3D report (report.html):

  • a 3D viewer (Mol*) with all the binding surfaces on the structure and, with Next, each binding surface coloured by residue probability, from white (0) to red (1);
  • a table of the binding surfaces with their number of interfaces and residues, their top residues and their partners, and a table of the probabilities of all residues; click a column header to sort a table;
  • the dendrogram of the clustering and the residue probabilities along the sequence;
  • with the partner clustering, the bar plots of each binding surface for each type of annotation.

For an example, see the example report of trypsin (P00760), with the three partner clusterings.

Files

The download contains all the files of the job, among which:

File Content
report.html, state.mvsj The report and its 3D views
clustered_interfaces.out The interfaces of each binding surface
clustered_residues_probs.out The residues of each binding surface, ranked by probability
<pdb>-<chain>_cl<N>.pdb The structure, with the probabilities of binding surface N as B-factors
retrieved_interfaces.out All the retrieved interfaces
dendrogram_<linkage>.png The dendrogram of the clustering
sequence_probability.html The residue probabilities along the sequence
arctic3d-localise-<type>/ The partner clustering of each type
arctic3d.log The log of the job

See Result interpretation for how to read them.

To view report.html from the download, serve its directory with python -m http.server -d <directory> and open http://localhost:8000/report.html: browsers do not let a page opened from disk load the files of the 3D viewer.

If a job fails

The results page shows the output of the job, which often says why it failed (for example a UniProt ID without interfaces in the PDBe). For help, ask at https://ask.bioexcel.eu.

Running ARCTIC-3D locally

ARCTIC-3D is also available as a stand-alone program: see Installation and Examples.

References

To cite ARCTIC-3D, please refer to: