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CPHmodels 3.2 Server

CPHmodels 3.2 is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions.

New in version 3.2: An improvement in the alignment algorithm in case of remote homology modeling where a structure dependant gap penalty has been introduced. Also, there are changes in the output format. A summary line has been included to make parsing easier.

View the version history of this server.

Instructions Output format Article abstract


Paste a single sequence or several sequences in FASTA format into the field below:

Submit a file in FASTA format directly from your local disk:

Only one sequence per submission with not less than 15 and not more than 4,000 amino acids.

The sequences are kept confidential and will be deleted after processing.


For publication of results, please cite:

CPHmodels-3.0 - Remote homology modeling using structure guided sequence profiles
Nielsen M., Lundegaard C., Lund O., Petersen TN
Nucleic Acids Research, 2010, Vol. 38, doi:10.1093/nar/gkq535
View the abstract.

CPHmodels 2.0: X3M a Computer Program to Extract 3D Models.
O. Lund, M. Nielsen, C. Lundegaard, P. Worning
Abstract at the CASP5 conferenceA102, 2002.

View the abstract.


Scientific problems:        Technical problems: