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MSA Generation Method
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Prediction Methods

D. T. Jones (1999) Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292, 195-202.
J. A. Cuff and G. J. Barton (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40, 502-511.
M. Ouali and R. D. King (2000) Cascaded multiple classifiers for secondary structure prediction. Protein Science 9, 1162-1176.
B. Rost (2001) Protein secondarystructure prediction continues to rise. Journal of Structural Biology 134, 204-218.
A. N. Lupas, M. Van Dyke and J. Stock (1991) Predicting Coiled Coils from Protein Sequences. Science 252, 1162-1164.
G. E. Tusnády and I. Simon (1998) Principles Governing Amino Acid Composition of Integral Membrane Proteins: Applications to Topology Prediction. Journal of Molecular Biology 283, 489-506.
Timothy Nugent, David T. Jones (2009) Transmembrane protein topology prediction using support vector machines BMC Bioinformatics 2009
Lukas Käll, Anders Krogh and Erik L. L. Sonnhammer. A Combined Transmembrane Topology and Signal Peptide Prediction Method. Journal of Molecular Biology 338(5):1027-1036, May 2004.
PrediSi: prediction of signal peptides and their cleavage positions. Hiller K, Grote A, Scheer M, M√ľnch R, Jahn D. Nucleic Acids Res 1;32, W375-9,Jul 2004.
J. J. Ward, J. S. Sodhi, L. J. McGuffin, B. F. Buxton and D. T. Jones (2004) Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life. Journal of Molecular Biology 337(3), 635-45.
Zsuzsanna Dosztá, Veronika Csizmók, Péter Tompa and István Simon (2005) The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins J. Mol. Biol. 347, 827-839.

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References (please cite as appropriate)

Alva V., Nam SZ., Söding J., Lupas AN. (2016) The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res. pii: gkw348. [Epub ahead of print] PMID: 27131380


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