pKNOT v.2: the protein KNOT web server

Yan-Long Lai, Chih Chieh Chen, Jenn-Kang Hwang

Research output: Contribution to journalArticle

22 Scopus citations


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
Original languageEnglish
Pages (from-to)W228-W231
Number of pages4
JournalNucleic Acids Research
Issue numberW1
StatePublished - Jul 2012



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