Team:NYMU-Taipei/modelling-protein-structure-champ-design

From 2011.igem.org

Revision as of 10:01, 4 October 2011 by Evelyn132 (Talk | contribs)

Modelling Protein Structure: CHAMP design

 

References

 

* Hang Yin, Joanna S. Slusky, Bryan W. Berger, Robin S. Walters, Gaston Vilaire, Rustem I. Litvinov, James D. Lear, Gregory A. Caputo, Joel S. Bennett, William F. DeGrado (2007). Supporting Online Material for Computational Design of Peptides That Target Transmembrane Helices. Science 315, 1817.

 

*J. S. Slusky, H. Yin and W. F. DeGrado (2009). Understanding Membrane Proteins. How to Design Inhibitors of Transmembrane Protein—Protein Interactions. PROTEIN ENGINEERING Nucleic Acids and Molecular Biology 22, 315-337.

 

* Lo A., Chiu Y.Y., Rødland E.A., Lyu P.C., Sung T.Y., and Hsu W.L. (2009) Predicting helix-helix interactions from residue contacts in membrane proteins. Bioinformatics 25, 996-1003.

 

* Lukasz Jaroszewski, Zhanwen Li, Xiao-hui Cai, Christoph Weber, and Adam Godzik. (2011) FFAS server: novel features and applications. Nucleic Acids Res. 39, W38–W44.

 

*Krieger E, Vriend G. (2002) Models@Home: distributed computing in bioinformatics using a screensaver based approach. Bioinformatics 18(2), 315-8.

 

*Krieger E, Koraimann G, Vriend G. (2002) Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field. Proteins 47(3):393-402.

 

*Krieger E, Nabuurs SB, Vriend G. (2003) Homology modeling. Methods Biochem Anal.44:509-23.

 

*Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. (2009) Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Protein 77 Suppl 9:114-22.

 

*Venselaar H, Joosten RP, Vroling B, Baakman CA, Hekkelman ML, Krieger E, Vriend G. (2010) Homology modelling and spectroscopy, a never-ending love story. Eur Biophys J. 39(4):551-63.

 

*Joosten RP, te Beek TA, Krieger E, Hekkelman ML, Hooft RW, Schneider R, Sander C, Vriend G. (2011) A series of PDB related databases for everyday needs. Nucleic Acids Res. 39(Database issue):D411-9.

 

*William Humphrey, Andrew Dalke, and Klaus Schulten. (1996) VMD – Visual Molecular Dynamics. Journal of Molecular Graphics 14:33-38.

 

* R. Sharma, T. S. Huang, V. I. Pavlovic, K. Schulten, A. Dalke, J. Phillips, M. Zeller, W. Humphrey, Y. Zhao, Z. Lo, and S. Chu. (1996) Speech/gesture interface to a visual computing environment for molecular biologists. In Proceedings of 13th ICPR 96, volume 3, pp. 964-968.

 

* Rajeev Sharma, Michael Zeller, Vladimir I. Pavlovic, Thomas S. Huang, Zion Lo, Stephen Chu, Yunxin Zhao, James C. Phillips, and Klaus Schulten. (2000) Speech/gesture interface to a visual-computing environment.  IEEE Computer Graphics and Applications 20:29-37.

 

* David J. Hardy, John E. Stone, and Klaus Schulten. Multilevel summation of electrostatic potentials using graphics processing units. Journal of Parallel Computing 35:164-177.

 

* Hessa, T., Meindl-Beinker, N., Bernsel, A., Kim, J., Sato, Y., Lerch, M., Lundin, C., Nilsson, I., White, SH. and von Heijne, G. (2007) Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature. 450, 1026-1030.

 

* Hessa, T., Kim, H., Lundin, C., Boekel, J., Andersson, H., Nilsson, I., White, SH. and von Heijne, G. (2005) Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433, 377-381.

 

* Dieter Langosch, Jana R. Herrmann, Stephanie Unterreitmeier and Angelika Fuchs. (2009) Structural Bioinformatics of Membrane Proteins- Helix-helix interaction patterns in membrane proteins.

 

* Dieter Langosch, Isaiah T. Arkin. (2009) Interaction and conformational dynamics of membrane-spanning protein helices. Protein Science 18: 1343–1358.

 

* Hirokawa T., Boon-Chieng S., and Mitaku S. (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics, 14:378-9.

 

*Mitaku S., Hirokawa T. (1999) Physicochemical factors for discriminating between soluble and membrane proteins: hydrophobicity of helical segments and protein length. Protein Eng. 11.

 

* Mitaku S., Hirokawa T., and Tsuji T. (2002) Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces. Bioinformatics, 18:608-16.

 

*M. Cserzo, E. Wallin, I. Simon, G. von Heijne and A. (1997) Elofsson: Prediction of transmembrane alpha-helices in procariotic membrane proteins: the Dense Alignment Surface method. Prot. Eng. vol. 10, no. 6: 673-676.

 

*Krogh A, Larsson B, von Heijne G, Sonnhammer EL. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 305(3):567-80.

 

*Laszlo Kajan, Yachdav, G., Burkhard, R. (2011). High-throughput protein feature prediction in the cloud. Bioinformatics (submitted).

 

*K. Hofmann & W. Stoffel. (1993)TMbase - A database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler:374,166.

 

*G.E Tusnády and I. Simon (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17:849-850.

 

* Nugent, T. & Jones, D.T. (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics. 10:159. Epub.

 

*Jones DT. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics. 23: 538-544.

 

*Jones DT, Taylor WR, Thornton JM. (1994) A Model Recognition Approach to the Prediction of All-Helical Membrane Protein Structure and Topology. Biochem. 33: 3038-3049.

 

* Gunnar von Heijne. (1992) Membrane Protein Structure Prediction, Hydrophobicity Analysis and the Positive-inside Rule. J. Mol. Biol. 225:487-494.

 

* William P Russ, Donald M Engelman. (2000) The GxxxG motif: A framework for transmembrane helix-helix association. Journal of Molecular Biology 296, Issue 3: 911-919

* Alessandro Senes, Iban Ubarretxena-Belandia, and Donald M. Engelman. (2001) The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions. Proc Natl Acad Sci USA.31; 98(16): 9056–9061.

 

* R. F. S. Walters and W. F. DeGrado. (2006) Helix-packing motifs in membrane proteins. PNAS vol. 103 no. 37:13658-13663.

 

* Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K Proteins. (2009) Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins.77 Suppl 9:114-22.