
NNSSP Program Description Version 2.NNSSP  Prediction of protein secondary structure by combining nearestneighbor algorithms and multiply sequence alignmentsVersion 2 Method description:Yi and Lander (*) developed a neuralnetwork and nearestneighbor method with a scoring system that combined a sequence similarity matrix with the local structural environment scoring scheme of Bowie et al.(**) for predicting protein secondary structure. We have improved their scoring system by taking into consideration N and Cterminal positions of ahelices and bstrands and also bturns as distinctive types of secondary structure. Another improvement, which also significantly decrease the time of computation, is performed by restricting a data base with a smaller subset of proteins which are similar with a query sequence. Using multiple sequence alignments rather than single sequences and a simple jury decision method we achieved an over all threestate accuracy of 72.2%, which is better than that observed for the most accurate multilayered neural network approach, tested on the same data set of 126 nonhomologous protein chains. (*) Yi TM., Lander E.S. (1993)
(**) Bowie J.U., Luthy R., Eisenberg D. (1991)
Accuracy: SEE ALSO "ssp" program of this server. Example of NNSSP output: This output contains probabilities (Pa and Pb) of a and b structures in 09 scale. Probability of c is approximately 10  Pa  Pb. ADENYLATE KINASE ISOENZYME3, /GTP:AMP$ L= 214 SS content: a 0.43 b= 0.05 c= 0.52 10 20 30 40 50 PredSS aaaaaaa aaaaaa aaaaaaaa aa AA seq RLLRAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLA Prob a 99888651000001112244545422211111346775554221332335 Prob b 00001221000001134422321222233221001110010101134443 60 70 80 90 100 PredSS aaaa aaaaaaaaaaaaaaaa aaaaaaaaa AA seq KTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAY Prob a 54543201110346789888877545553334210001113588888875 Prob b 22221001210001111000000000111233410101110000000011 110 120 130 140 150 PredSS bb aaaaaaaa bb bbbb AA seq QIDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTMGIDDLTGE Prob a 32111111111466766643321110001100000000000111111111 Prob b 12135643321222110122245531001478764210013333211101 160 170 180 190 200 PredSS aaaaaaaaaaaaaaaaaaaaaaa bbb a AA seq PLVQREDDRPETVVKRLKAYEAQTEPVLEYYRKKGVLETFSGTETNKIWP Prob a 23433211146788999997765577888886621121111111123335 Prob b 12321000001110000000000000000000101365542111111221 210 PredSS aaaaaaa AA seq HVYAFLQTKLPQRS Prob a 46687764210111 Prob b 22211110110001 Reference: Salamov A.A., Solovyev V.V.

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