Computational Chemistry
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SOPMA
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.
Free for academic users via Anonymous ftp to ibcp.fr
SOPMA accuracy
| STATES | Coil | Helix | Sheets | All |
|---|---|---|---|---|
| Accuracy | 77.50 | 72.20 | 65.40 | 73.20 |
| Std. Dev | 9.43 | 8.66 | 8.98 | n/a |
| Correl. Coeff. Matthews Coefficients |
0.54 | 0.62 | 0.57 | n/a |
| SOV Coeffic. | 0.67 | 0.74 | 0.78 | 0.71 |
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, Submitted
Secondary structure prediction by SOPMA can be performed by us provided you send the sequence (just the sequence) by Email to deleage@ibcp.fr with "SOPMA" as the subject or use our WWW server (URL http://www.ibcp.fr)
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 6 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)
Submitted
Rost & Sander, (1994) Proteins, 19, 55-72.
Kneller et al., (1990) J. Mol. Biol. 214, 171-182
The PHD mail server (used for consensus) is described in: Rost et al. (1994) CABIOS, Vol. 10, pp. 53-60.
2) An extensive search for sites is provided using the PATTERN program (PROSITE) Geourjon & Deleage (1993) CABIOS, 9, 87-91
Contact info
Release 2.0 (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@ibcp.fr
geourjon@ibcp.fr
Web page : http://www.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
