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##### elf #######ptimised #rediction # #ethod from # #lignments
by
C. Geourjon & G. Deleage
Institut de Biologie et Chimie des Proteines
IBCP-CNRS UPR 412
Groupe de modelisation et RMN
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.frgeourjon at ibcp.fr
Web page : http://www.ibcp.fr
Don't hesitate to contact us in case of problems, bugs or suggestions.
SOPMA (Self Optimized Prediction Method from Alignment) 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 and SGI.
========================= SOPMA availability ================================
Free for academic users:
Anonymous ftp to ibcp.fr
For companies inquire to:
Mr R. Lahana
Oxford Molecular SA
X- Pole Ecole Polytechnique
F-91128 PALAISEAU Cedex
Tel: 33 1 69 33 35 90
Fax: 33 1 69 33 30 41
========================= SOPMA accuracy ================================
As checked on our SOPM.BASE (233 proteins chains)
+--------------------------+---------+----------+----------+-----------+
| States | Coil | Helix | Sheet | All |
+--------------------------+---------+----------+----------+-----------+
| Accuracy | 77.50 | 72.20 | 65.40 | 73.20 |
| | | | | |
| Standard deviation | 9.43 | 8.66 | 8.98 | - |
| | | | | |
| Correlation Coeficients | 0.54 | 0.62 | 0.57 | - |
| (Matthews coeficient) | | | | |
| | | | | |
| SOV Coeficients | 0.67 | 0.74 | 0.78 | 0.71 |
+--------------------------+---------+----------+----------+-----------+
As checked on Rost and Sander database (126 proteins chains)
+--------------------------+---------+----------+----------+-----------+
| States | Coil | Helix | Sheet | All |
+--------------------------+---------+----------+----------+-----------+
| Accuracy | 74.80 | 70.40 | 60.30 | 69.50 |
| | | | | |
| Standard deviation | 12.00 | 12.00 | 10.80 | - |
| | | | | |
| Correlation Coeficients | 0.48 | 0.56 | 0.51 | - |
| (Matthews coeficient) | | | | |
| | | | | |
| SOV Coeficients | 0.63 | 0.74 | 0.72 | 0.68 |
+--------------------------+---------+----------+----------+-----------+
========================= SOPMA references ================================
1/ A brief description is given in:
"SOPM : a self optimised prediction method for protein
secondary structure prediction."
C. Geourjon & G. Deleage, 1994, Protein Engineering, 7, 157-164
2/ Latest improvement steps and SOPMA mail server are explained in:
"SOPMA : Significant improvements in protein secondary
structure prediction by prediction from multiple alignments."
C. Geourjon & G. Deleage, 1995, Comput. Appli. Biosc., In press
========================= SOPMA by mail ===================================
Secondary structure prediction by SOPMA can be performed by us provided you
send the sequence (just the sequence) by Email to deleage at ibcp.fr with
"SOPMA" as the subject or use our WWW server http://www.ibcp.fr/predict.html
Warning: The body of the message must contain just the sequence (no blank,
no title, no signature, no special characters *,>,...)
In this case, you should receive 2 files:
1) A consensus secondary structure derived from 5 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
(1995) Comput. Appli. Biosc., In press
Rost & Sander (1994) Proteins, 19, 55-72.
The PHD mail server (used for consensus) is described in:
Rost et al. (1994) CABIOS, Vol. 10, pp. 53-60.
If the PHD prediction is not available with reasonable response time, the
consensus is calculated from the 4 first methods.
In the prediction (H, G Helix ; E, Sheet ; T, Turn ; C, coil ; S ,Bend; B
bridges).
2) An extensive search for sites is provided using the
PATTERN program (PROSITE)
Geourjon & Deleage (1993) Comput. Appli. Biosc., 9, 87-91
========================= SOPMA users ==================================
Could you send us your adress (Email is prefered) and your feelings about
your SOPMA 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 #
=====================================================================
