HMMSTR/I-sites/Rosetta Prediction Server
About HMMSTR/I-sites/Rosetta


by Chris Bystroff , Vesteinn Thorsson , and David Baker

Server developed with help from Yu Shao and Kirsten Piotrowski
Click on the title for more information

Click here to see how many jobs are in the queue

HMMSTR says: Several cluster nodes were moved to new IP addresses recently. If you had problems, please resubmit.

Email address to which results are to be sent:

Check your spelling! If the address is wrong, you will receive no messages!

Add a short identifying remark for this sequence:

Type or paste your amino acid sequence information below. SPECIFY INPUT FORMAT:
Single sequence in 1-letter code. PDB format. Use PSI-BLAST to generate alignment. Use a low-complexity filter.
--- or ---
Multiple sequence alignment file in HSSP FASTA Clustal SAF format:

Optional chain identifier:

Output options:
A multiple sequence alignment in SAF format (only if using PSI-BLAST). example
Sequence names and weights used for generating the sequence profile. example
A set of multiple, predicted fragments sorted by confidence. example
A set of predicted backbone angles and confidences based on linking fragments. example
A one-dimensional prediction of backbone angle (phi/psi) regions based on linked fragments. example
A prediction of 3-state secondary structure, backbone angles and context symbols using HMMSTR.   example
A set of 3D coordinates in PDB format, generated using ROSETTA. example

===========EXPERT SETTINGS===========

Method to use: Use PHD + I-sites example Use I-sites ONLY
HMMSTR model to use: C
Maximum e-value for PSI-BLAST:
Window size for SEG filter:
Low-complexity cutoff for SEG filter:
Ignore I-sites shorter than in fragment prediction report.
Minimum allowed percent identity for inclusion in profile :
Minimum allowed confidence of fragment prediction:
Number of parent sequence in an input multiple alignment (usually 1) :
Look for a homolog of known structure using Psi-Blast (non ab-initio prediction!):
Label :
Number output coordinates starting from:


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Last updated: Wed Dec 18 15:05:10 EST 2002