Difference between revisions of "Quick2D"
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;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. | ;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. | :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 '''b'''uried residue has at most 25% of its surface exposed to the solvent.) | ||
==External links== | ==External links== | ||
Latest revision as of 18:29, 24 June 2008
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.)
