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Structural Modeling for a Primary Circular Permutant


* Format: PDB + chain ID. If there is no chain ID,
input 4-letter code or use '_' for the chain ID.
Example: 1rx4A, 1jul, 1HEL_

& Chain ID in this file:
* If there is no chain ID, please leave it blank or use '_'.

CP site: (required) * Here a CP site also means the starting residue of the simulated circular permutant.
For instance, CP site = 10 means that the original residue 10
will be the first residue of the simulated circular permutant.

Sequence of the inserted linker (optional):

* Format: FASTA or a raw sequence


CirPred is the first structure modelling and linker design system for a powerful protein engineering technique known as circular permutation (CP), which can be visualized as if the native termini of a protein were linked and new ones created elsewhere.

We have previously developed CPred and (PS)2, a viable CP site predictor and a protein structure prediction system, respectively. Here we integrate the artificial intelligence methods applied in CPred and the modelling algorithm of (PS)2, along with MODELLER and Gromacs, and present the CirPred.

Chen CC, Hwang JK, Yang JM: (PS)2: protein structure prediction server.
Nucleic Acids Research 2006, doi:10.1093/nar/gkl187. [
Abstract] [PDF]

Lo WC, Wang LF, Liu YY, Dai T, Hwang JK, Lyu PC: CPred: a web server for predicting viable circular permutations in proteins.
Nucleic Acids Research 2012, doi:10.1093/nar/gks529. [Abstract] [PDF]

Lo WC, Lee CC, Lee CY, Lyu PC: CPDB: a database of circular permutation in proteins.
Nucleic Acids Research 2009, 37:D328-332. [Abstract] [PDF]

Lo WC, Lyu PC: CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships.
Genome Biology 2008, 9:R11. [Abstract] [PDF]