Prediction of protein secondary structure by using local alignments. New, improved accuracy version with current PDB proteins was installed on October 3, 2001
Overall 3-state (a, b, c) prediction gives about 75% correctly predicted residues. THIS ACCURACY IS REACHED WITHOUT USING MULTIPLE ALIGNMENT INPUT when it is higher SEE ALSO "ssp" and "nssp" programs of this server.
Output results with probability of prediction:
Length=136 10 20 30 40 50 PredSS aaaaaaaaaaaa aaaaaaaaaaa aaaa aaaa AA seq LSADQISTVQASFDKVKGDPVGILYAVFKADPSIMAKFTQFAGKDLESIK ProbA 11999999999999111119999999999919999111111111199991 ProbB 11000000000000111110000000000010000111111111100001 60 70 80 90 100 PredSS aaaaaaaaaaaaaaaaaaa aaaaaaaaaaa aaaaaaa AA seq GTAPFETHANRIVGFFSKIIGELPNIEADVNTFVASHKPRGVTHDQLNNF ProbA 11999999999999999999911111999999999991111119999999 ProbB 11000000000000000000011111000000000001111110000000 110 120 130 PredSS aaaaaaaaaaa aaaaaaaaaaaaaaaaaa AA seq RAGFVSYMKAHTDFAGAEAAWGATLDTFFGMIFSKM ProbA 999999999991111119999999999999999991 ProbB 000000000001111110000000000000000001
You can input multiple aligned sequences (now only in local version or email servers)
The number of aligned sequences must be less than 250 !!!
for example:
ACTINOXANTHIN 5 107 10 20 30 40 50 60 (numbers not APAFSVSPASGASDGQSVSVSVAAAGETYYIAQaAPVGGQDAaNPATATSFTTDASGAAS necessary) APAFSVSPASGLSDGQSVSVSGAAAGETYYIAQCAPVGGQDACNPATATSFTTDASGAAS APTATVTPSSGLSDGTVVKVAGAgaGTAYDVGQCAWVdgVLACNPADFSSVTADANGSAS APGVTVTPATGLSNGQTVTVSATgpGTVYHVGQCAVvpGVIGCDATTSTDVTADAAGKIT ATPKSSSGGAGASTGSGTSSAAVTSgaASSAQQSGLQGATGAGGGSSSTPGTQPGSGAGG 70 80 90 100 FSFTVRKSYAGQTPSGTPVGSVDbATDAbNLGAGNSGLNLGHVALTF FSFV-RKSYAGZTPSGTPVGSVDCATDACNLGAGNSGLNLGHVALTF TSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGpgVAISF AQLKVHSSFQAVvaNGTPWGTVNCKVVSCSAGLGSDSGEGAAQAITF AIAARPVSAMGGtpPHTVPGSTNTTTTAMAGGVGGPgaNPNAAALM- (you can use small letters for Cys amino acids, if you want) Alignment MUST be without deletions in the 1-st (query) sequence!!!
Reference:
Salamov A.A., Solovyev V.V.
Protein secondary sturcture prediction using local alignments.
J.Mol.Biol.1977, 268,1, 31-36.
Salamov A.A., Solovyev V.V.
Prediction of protein secondary sturcture by combining nearest-neighbor algorithms
and multiply sequence alignments.
J.Mol.Biol.1995,247,1,11-15.
New version is implemented in collaboration with Drs. A. Bachinskiy and V. Ivanisenko