pKNOT v.2: the protein KNOT web server.
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/.
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan, Republic of China.
Yan-Long
YL
Lai
Chih-Chieh
CC
Chen
Jenn-Kang
JK
Hwang
D020407:Internet; D011487:Protein Conformation; D020539:Sequence Analysis, Protein; D012984:Software; D040681:Structural Homology, Protein