The LOOPP (Learning, Observing and Outputting
Protein Patterns) server. LOOPP is a fold recognition program based on the
collection of numerous signals, merging them into a single score, and
generating atomic coordinates based on an alignment into a homologue template
structure. The signals we are using include straightforward sequence alignment,
sequence profile, threading, secondary structure and exposed surface area
prediction. For more information please refer to the
LOOPP home page.
LOOPP HAS BEEN UPGRADED. We have upgraded LOOPP to the newest version just in time for CASP8. The new version is much better than the previous one, it uses new scoring technique as well as upgraded database. The improvemnets are descibed in the upcoming Proteins paper.
NOTE ABOUT CASP8.
This server is participating in CASP8 experiment. All LOOPP predictions for CASP8 targets with the default server parameters are available online
here. Please don't submit CASP8 targets again with default parameters -
just use the link!
If you
have any comments or questions about LOOPP please contact us at
loopp@tc.cornell.edu.
It may take several hours to run this program.
Calculations will be carried out on the BioHPC compute cluster at CBSU. You will receive e-mail notifications when the job is submitted, when it starts, and when it is finished. Output will be available via links embedded in the notification e-mails. For more information about this program and BioHPC interface in general, please visit our Frequently Asked Questions page.
Please acknowledge us in all publications and presentation of work
that used our resources using the following
text.
Job name:
(please,
no spaces, special characters etc., uderscore is OK)
Please notify me
about LOOPP updates
Input sequence (amino acids
one-letter code only, no names, numbers etc):
Cluster:
Nodes:
(0
means that the number of nodes will be chosen automatically)
(
Show timeout info )
