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Institut de Biologie et Chimie des Proteines
IBCP-CNRS UPR 412
Molecular modeling and NMR group
7, Passage du vercors
69 367 Lyon cedex 07
France
Tel : (33) 72 72 26 47
Fax : (33) 72 72 26 01
deleage at ibcp.fr, pilote at ibcp.fr
by C. Geourjon & G. Deleage
SOPM (Self Optimized Prediction Method) is a package
to make secondary structure predictions of proteins. This program is
developed for Unix workstations and has been successfully checked onto IBM
rs6000 workstations, SUN and SGI.
========================= SOPM availability ================================
Free for academic users:
Anonymous ftp to ibcp.fr
Directory: pub/SOPM
========================= SOPM accuracy ================================
Coil Helix Sheet All
Accuracy
74.0 66.3 60.9 69.0
Standard deviations
9.85 11.09 9.99
Correlation coeficients
.49 .53 .51
========================= SOPM by mail ===================================
Secondary structure prediction by SOPM can be performed by us provided you
send the sequence (just the sequence) by Email to deleage at ibcp.fr with
"predict" as the subject. In this case, you should receive 5 files:
Warning: The body of the message must contain just the sequence (no blank,
no title, no signature, no special characters *,>,...)
1) SOPMANSWER
2) An abstract of SOPM analysis (H=helix,E=Sheet,C=Coil)
3) A detailed prediction by SOPM
4) A consensus secondary structure derived from 4 methods
Gibrat et al., (1987) J.Mol.Biol. 198, 425-443
Levin et al., (1986) Febs Lett. 205, 303-308
Deleage & Roux (1987) Prot. Engng. 1, 289-294
Geourjon & Deleage (1994) Prot. Engng. 7, 157-164
5) An extensive search for sites is provided using the
PATTERN program (PROSITE)
Geourjon & Deleage (1993) CABIOS, 9, 87-91
========================= SOPM users ================================
Could you send us your feelings about your SOPM experience?
Many thanks
--
=====================================================================
# Institut de Biologie et Chimie des Proteines. UPR 412-CNRS #
# ***** ***** **** ***** Dr Gilbert Deleage #
# # # # # # # # 7, passage du Vercors #
# # ***** # # # 69367 Lyon Cedex 07,FRANCE #
# # # # # #**** Tel: (33) 72-72-26-47 #
# # # # # # # Fax: (33) 72-72-26-01 #
# ***** ****** **** # deleage at ibcp.fr #
=====================================================================
