Ab initio protein folding

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. 

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. 

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... 

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. 

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

Ab Initio Protein Structure Prediction Using a Size-Dependent Tertiary Folding Potential 223... 

The most ambitious approaches to the protein folding problem attempt to solve it from firs principles (ab initio). As such, the problem is to explore the coirformational space of th molecule in order to identify the most appropriate structure. The total number of possibl conformations is invariably very large and so it is usual to try to find only the very lowes energy structure(s). Some form of empirical force field is usually used, often augmente with a solvation term (see Section 11.12). The global minimum in the energy function i assumed to correspond to the naturally occurring structure of the molecule. 

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

ES Huang, P Koehl, M Levitt, RV Pappu, JW Ponder. Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods. Proteins 33 204-217, 1998. 

The use of the term ab initio in the context of protein folding should not be confused with its use to describe ab initio quantum chemistry calculations. In both cases, ab initio is meant to convey the idea of from first principles, but die starting point and theoretical framework are different for each. 

In another study of protein structure, Cox and Johnston3 analyzed how the choice of GA parameters affects the quality of the GA search. This sort of approach was also adopted by Djurdjevic and Biggs,4 who presented a detailed study of how evolutionary algorithms can be used, in combination with a full atomistic protein ab initio model, for fold prediction and, like Cox and Johnston, considered the influence of the different values of parameters on the success of their protein folding calculations. 

Liwo A, Khalili M, Scheraga HA (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. 

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