Quick2D

Quick2D is an Online server that gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2, and VSL2.

Features

PSIPRED 

D. T. Jones (1999) Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292, 195-202.

JNET 

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.

PROF 

M. Ouali and R. D. King (2000) Cascaded multiple classifiers for secondary structure prediction. Protein Science 9, 1162-1176.

PROF 

B. Rost (2001) Protein secondarystructure prediction continues to rise. Journal of Structural Biology 134, 204-218.

COILS 

A. N. Lupas, M. Van Dyke and J. Stock (1991) Predicting Coiled Coils from Protein Sequences. Science 252, 1162-1164.

MEMSAT2 

D. T. Jones, W. R. Taylor and J. M. Thornton (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33, 3038-3049.

HMMTOP 

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.

DISOPRED2 

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.

VSL2 

K. Peng, P. Radivojac, S. Vucetic, A. K. Dunker, and Z. Obradovic (2006), Length-Dependent Prediction of Protein Intrinsic Disorder. BMC Bioinformatics 7, 208.

Z. Obradovic, K. Peng, S. Vucetic, P. Radivojac, and A. K. Dunker, Exploiting Heterogeneous Sequence Properties Improves Prediction of Protein Disorder (2005). Proteins 61(S7), 176-182.

Results

• SS = Alpha-Helix / Beta-Sheet Secondary Structure
• CC = Coiled Coils
• TM = Transmembrane ('+'=outside, '-'=inside)
• DO = Disorder
• SO = Solvent accessibility (A buried residue has at most 25% of its surface exposed to the solvent.)

External links

• Quick2D Server