Protein structure predictions

S. Sun, Reduced representation model of protein structure prediction statistical potential and genetic algorithms. Protein Sci. 2 (1993), 762-785. 

P. Ulrich, W. Scott, W.F. van Gunsteren and A. Torda, Protein structure prediction force 6elds parametrization with quasi Newtonian dynamics. Proteins 27 (1997), 367-384. 

Protein Structure Prediction, Sequence Analysis and Protein Folding... 

Ihe rule-based approach to protein structure prediction is obviously very reliant on th quality of the initial secondary structure prediction, which may not be particularly accurate The method tends to work best if it is known to which structural class the protein belongs this can sometimes be deduced from experimental techniques such as circular dichroism... 

A Comparison of Protein Structure Prediction Pilethocls CASP-... 

CASP stands for Critical Assessment of techniques for protein Structure Prediction. 

Moult J, T Hubbard, K Fldelis and J T Pedersen 1999. Critical Assessment of Methods of Protein Structure Prediction (CASP) Round III. Proteins Structure, Function and Genetics Suppl. 3 2-6. 

GJ Barton. Protein sequence alignment and database scanning. In MJE Sternberg, ed. Protein Structure Prediction A Practical Approach. Oxford, UK IRE Press at Oxford Univ Press, 1998. 

MJE Sternberg, PA Bates, LA Kelley, RM MacCallum. Progress m protein structure prediction Assessment of CASP3. Curr Opm Struct Biol 9 368-373, 1999. 

J Moult, T Flubbard, SFI Bryant, K Fidelis, JT Pedersen. Critical assessment of methods of protein structure prediction (CASP) Round II. Proteins Suppl 1 2-6, 1997. 

RL Dunbrack Jr, DL Gerloff, M Bower, X Chen, O Lichtarge, FE Cohen. Meeting review The second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar, CA, Dec 13-16, 1996. Folding Des 2 R27-R42, 1997. 

Bowie, J.U., Eisenberg, D. Inverted protein structure prediction. Curr. Opin. Struct. Biol. 3 437-444, 1993. 

The strongest verification for a 3D-protein model comes from the experimental 3D-structure. This is the objective of the Critical Assessment of Techniques for Protein Structure Prediction, CASP ( http //predic tioncenter.org), where the structural models are made in advance of the experimental structure of a particular protein. 

The protein structure prediction problem refers to the combinatorial problem to calculate the 3D structure of a protein from its sequence alone. It is one of the biggest challenges in structural bioinformatics. 

Einkelstein AV, Gutin AM, Badretdinov AY. Perfect temperature for protein structure prediction and folding. Proteins 1995 23 151-62. 

Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CEM, et al. Rosetta in CASP4 Progress in ab initio protein structure prediction. Proteins 2001 119-26. 

Unger R (2004) The Genetic Algorithm Approach to Protein Structure Prediction 110 153-175... 

Bonneau R, Baker D (2001) Ab initio protein structure prediction progress and prospects. Annu Rev Biophys Biomol Struct 30 173-189... 

Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294(5540) 93-96... 

Skolnick J (2006) In quest of an empirical potential for protein structure prediction. Curr Opin Struct Biol 16(2) 166—171... 

Koehl, P. and Levitt, M. (1999), A brighter future for protein structure prediction , Nature, Struct. Biol., 6, 108-111. 

Fukunishi, O. Watanabe Takada, S., On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems application to protein structure prediction, J. Chem. Phys. 2002,116, 9058-9067... 

Haliloglu, T. Kolinski, A. Skolnick, J., Use of residual dipolar couplings as restraints in ab initio protein structure prediction, Biopolymers 2003, 70, 548-562... 

Westhead DA et al. Protein structure prediction. Curr Opin Biotechnol 1998 9 383-389. 

Al-Lazikani, B., Jung, J., Xiang, Z., and Honig, B. 2001. Protein structure prediction. Current Opinion in Chemical Biology 5(1), 51-56. 

Petrey, D. and Honig, B. 2005. Protein structure prediction inroads to biology. Molecular Cell 20(6), 811-819. Radford, S. 2000. Protein folding progress made and promises ahead. Trends in Biochemical Sciences 25(12), 611-618. 

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