Ab initio protein

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. 

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

Djurdjevic, D.P., and Biggs, N.J., Ab initio protein fold prediction using evolutionary algorithms Influence of design and control parameters on performance, /. Comp. Chem., Tl, 1177,2006. 

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

Koing, S. 2005. Functional protein analysis using mass spectrometry. Current Organic Chemistry 9(9), 875-887. Osguthorpe, D. 2000. Ab initio protein folding. Current Opinion in Structural Biology 10(2), 146-152. 

Bonneau, R., et al.. Functional inferences from blind ab initio protein structure predictions. J Struct Biol, 2001, 134(2-3), 186-90. 

Simons, K.T., Strauss, C., Baker, D. Prospects for ab initio protein structural genomics./. Mol. Biol. 2001, 1191-1199. 

Simons, K.T., Bonneau, R., Ruczinski, I., Baker, D. Ab initio protein structure prediction of CASP 111 targets using ROSETTA. Proteins 1999, 171-176. 

The GB method is regarded as a more computationally efficient approach to obtaining PB-like results at lower computational cost. The GB method has been applied to a variety of biomolecular computational problems including ab initio protein folding (33). The relevant equations for the MM-PBSA and MM-GBSA calculations are as follows (Eqs. 6-9) ... 

Wen EZ, Hsieh MJ, Kollman PA, Luo R (2004) Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self guiding forces, J Mol Graph Model, 22 415—424... 

Bystroiff, C., andY. Shao. 2002. Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA. Bioinformatics 18 S54—61. 

Simons K T, R Bonneau, I Ruszmski and D Baker 1999b. Ab Initio Protein Structure Prediction of CASP 111 Targets Using ROSETTA. Proteins Structure, Function and Genetics Supplement 3 171-176. 

Kihara, D., Lu, H., Kolinski, A., Skolnick, J. TOUCHSTONE An ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc. Natl. Acad. Sci. USA 2001, 98, 10125-30. 

Xu, Z., Lazim, R., Sun, T, Mei, Y, and Zhang, D. (2012). Solvent effect on the folding dynamics and structure of e6-associated protein characterized from ab initio protein folding simulations. The Joumai of Chemicai Physics 136,13, p. 135102. 

Brylinski M (2013) eVolver an optimization engine for evolving protein sequences to stabilize the respective structures. BMC ResNotes6 303. doi 10.1186/1756-0500-6-303 Zhang Y (2013) Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASPIO. Proteins (in press)... 

Various recently developed methods for ab initio protein structure predictions were tested during the CASP3 (Critical Assessment of Techniques for Protein Stmcture Prediction) exercises, concluded in December 1998 in Asilo-mar, California [127]. A number of new techniques have been developed before that time, and a number of them constitute qualitative progress in ab initio prediction with respect to the previous CASPs (held every two years). 

AB INITIO PROTEIN STRUCTURE PREDICTION USING A SIZE-DEPENDENT TERTIARY FOLDING POTENTIAL... 

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