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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@ibcp.fr
geourjon@ibcp.fr
Web page : http://www.ibcp.fr
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.
1 10 20 30 40 50 60
| | | | | | |
IBCP-Web server MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
Gibrat method HCCCCCCHHHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Levin method ECCCCCCCHHHHHHCCTTTCHHHHCCHHHHHHEEECCTCHCHHHHHHHHHHHHHHHHHHH
DPM method CCHCTCHHHHHHHCTTTCCCCCCCHCHHHHHHHEECCCTCCHHHHHHHHCHHCHHHHHHH
SOPMA predict CCCCCHHHHHHHHHHHCCHHHHHHHHHCCHHCCCCCCCTHHHHHHHHHHHHTTHHHHHHH
Consensus CCCCCCCHHHHHHHHCCCCCHHHHHCHHHHHHHEECCCTHCHHHHHHHHHHHHHHHHHHH
IBCP-Web server RELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
Gibrat method HHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCHEEHHHHCCCCCCCCCCCCEEEECCCC
Levin method HHHHHCHCHHHCHHHHHHHHHHSCEEEEECTTSCCCEECCSCCCCCTCCCCCCEEECTTS
DPM method HHHHHHHHTTCCECHEEHHHHHHHEEEHECCCCCEEECECCCCCCCCCCCCCHHHHHCCC
SOPMA predict HHHHHHHHHCCCHHHEEECCCHHHEEEEECCTTCEEEEETCCCCTHHHCCCCEEEHCCCC
Consensus HHHHHHHHHCCCHCHHHHHHHHHHEEEHECCCCCEEEEECCCCCCCCCCCCCEEEHCCCC
IBCP-Web server YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
Gibrat method HHHHHHCCCCCCCHHHHHHEECCCCCCHHEHHCCHHHHHHHHHHHHHHHCCHHHHHHHHH
Levin method ECEHTECCTCCCHHHEEEEEHCCCTCCHHEHHSCHHHHHHHHHHHHCCCSCCHHHHHHCC
DPM method CCCCCCCCCCCCCCEEHHHHHHCCCCCCCHCCCCCCHHHHHHHHEHHCCCCCHHHHHHCH
SOPMA predict CCCEEECTTTCCHHCTTEEETTCCCCEEEEHHCCCCCHHHHHHHHHHHCCCCCTEEEEEE
Consensus CCCH-ECCCCCCCHHEHHHEHCCCCCCHHEHHCCCCHHHHHHHHHHHCCCCCHHHHHHCH
IBCP-Web server AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
Gibrat method HCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCEEEEEHHCCHHHHHHHHHHHHH
Levin method CSCSEEEEECCCCSCHHHHHHHHHHCCCCEEEEECTHHHHHHHHHCTHHHHHHHHHHHTT
DPM method HCCCCECCCCCCTCCCCHHHHHHHHCCCCCEEEECTCHHEHHHECCCHHHHHHHHHHHHH
SOPMA predict EEETTEEEEECCCCCTHHHHHHHHHEEEEEEEECCCTHEEEEEEHCTHHHHHHHHHHHHH
Consensus HCCCCEEEECCCCCCHHHHHHHHHHCCCCEEEEECCCHHEHHHHHCCHHHHHHHHHHHHH
IBCP-Web server HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
Gibrat method CCCCHEEEEEECCCCEEEEECCCCCCCEHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH
Levin method CCCCCEEECHCSCCCCSCCCCCCTCCHHHHHHHHHHHHHHHHHHHHHCHHEEECTSCCCE
DPM method HHCCEEEHHHCCCCCTCCTTTTTTTTCCHHHHHHHHHCHHCCHHHCHCEHEEHHCCHCCC
SOPMA predict HCCEEEEEECCCCCCCCTECCCCCCCCTHHHHHHHHHHHHTCHHHHHHHHHEECTTTCCE
Consensus CCCCEEEEEHCCCCCCCCECCCCCCCC-HHHHHHHHHHHHHCHHHHHCHHHEHCTCCCCE
IBCP-Web server LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
Gibrat method HHHHHHCCCCECCEECCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCHCCCCCCEE
Levin method EHHHHHCTTCCCTCCCCCCCCCCHHEEEHHHCTSCCCCCTCCCHHHHHHHCTTCCCHHHH
DPM method HCCHHHCCCCCCHHHCCCCCCCHHHHHHHHECCHHHCCCCCCCHHHHHHHHCTTCCCHHC
SOPMA predict EHTTTCEECCCCEEECCCCCCHHHHHHHHHHHHHEEECCCCCCHHHHHHHETTTTTCEEE
Consensus HHHHHHCCCCCC-EECCCCCCCHHHHHHHHHCHHHHCCCCCCCHHHHHHHCTTCCCCHHE
IBCP-Web server GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK
Gibrat method EEEHHHCCHHEHHHEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Levin method HHCHHHHHHHHHHHCSCCCTHHHHHHHHHHHHSTHCCHHHHHHHHH
DPM method CECCHHCHHHHHHHHEHECHHHHHHHHHHHHHHTCCCTHCHHHHCC
SOPMA predict EEEEHHHEEHHHHHEEEEEHHHHHHHHHHHHHCCCCCCCCHHHHHH
Consensus EECHHHCHHHHHHHEEECCHHHHHHHHHHHHHCTCCCHHCHHHHHH
>Please in your publication cite :
"SOPM : a self optimised prediction method for protein secondary structure
prediction."
C. Geourjon & G. Deleage, 1994, Protein Engineering, 7, 157-164
"SOPMA : Significant improvements in protein secondary structure prediction by
prediction from multiple alignments."
C. Geourjon & G. Deleage, 1995, Comput. Applic. Biosci., 11, 681-684
Other methods :
Gibrat method : Gibrat et al., (1987) J.Mol.Biol. 198, 425-443
Levin method : Levin et al., (1986) Febs Lett. 205, 303-308
DPM method : Deleage & Roux, (1987) Prot. Engng. 1, 289-294
PhD method : Rost & Sander, (1994) Proteins, 19, 55-72
In the prediction :
H, G : Helix
E : Sheet
C : coil
S : Bend
B : bridges
========================= 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
