pKNOT v.2: the protein KNOT web server

Abstract

Knotted proteins have recently received lots of attention due to their interesting topological novelty as well as its puzzling folding mechanisms. We previously published a pKNOT server, which provides a structural database of knotted proteins, analysis tools for detecting and analyzing knotted regions from structures as well as a Java-based 3D graphics viewer for visualizing knotted structures. However, there lacks a convenient platform performing similar tasks directly from 'protein sequences'. In the current version of the web server, referred to as pKNOT v.2, we implement a homology modeling tool such that the server can now accept protein sequences in addition to 3D structures or Protein Data Bank (PDB) IDs and return knot analysis. In addition, we have updated the database of knotted proteins from the current PDB with a combination of automatic and manual procedure. We believe that the updated pKNOT server with its extended functionalities will provide better service to biologists interested in the research of knotted proteins. The pKNOT v.2 is available from http://pknot.life.nctu.edu.tw/.

Figure 1.

The yearly growth of knotted proteins in PDB from 1984 to 2011.

Figure 2.

The schematic work flow of pKNOT: accepting a query protein sequence, modeling a 3D structure through homology modeling (PS)² and smoothing out its backbone for the detection of its knot. The knot shown in this example is a 3₁knot.

Figure 3.

The features of the pKNOT v.2 web server: (A) STRUCTURE QUERY: users can enter PDB ID or upload PDB file. (B) SEQUENCE QUERY: users can enter or upload protein sequences in FASTA format. (C) Users can view the modeled structure in 3D graphics viewer and inspect its knot region.