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© Oxford University Press

An Excel spreadsheet computer program combining algorithms for prediction of protein structural characteristics

Josep Clotet 1, Juan Cedano 2 and Enrique Querol 1,2,3

1Departament de Bioquimica i Biologia Molecular, Villar Palasi, Universitat Autonoma de Barcelona 08193 Bellaterra, Barcelona, Spain
2Institut de Biologia Fonamental V, Villar Palasi, Universital Autonoma de Barcelona 08193 Bellaterra, Barcelona, Spain

3To whom correspondence should be addressed at. Institut de Biologia Fonamental, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain

A program running on personal computers (either Apple Macintosh or PC, using Excel worksheets) for the prediction of some protein structural characteristics is reported. The program runs according to the Chou and Fasman algorithm, with some modifications, for secondary structure prediction. The program also incorporates several complementary analyses for secondary structure prediction to help the user in the decision-making process: rules for amino acid preferences in the N-cap and C-cap of {alpha}-helices; prediction of the protein structural class and search of sequential motifs related to secondary structure. Additional algorithms performed by the program are: prediction of domain boundaries, prediction of loops, prediction of the state of cysteines (reduced or in disulfide bridge), hydropathy profiles according to Kyte and Doolittle, Hoop and Woods, and flexibility plot according to Karplus and Schulz.


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