From Protein Structure to Function with Bioinformatics.pdf

1 Ab Initio Protein Structure Prediction 11Fig. 1.2 Flowchart of the ROSETTA protocolcontrolling the protein radius of gyration. However, their prediction seems to beonly partially successful in comparison to ROSETTA.Another successful free modelling approach, TASSER by Zhang and Skolnick(2004a), constructs 3D models based on a purely knowledge-based approach. Thetarget sequence is first threaded through a set of representative protein structures tosearch for possible folds. Contiguous fragments (>5 residues) are then excised fromthe threaded aligned regions and used to reassemble full-length models, while unalignedregions are built by ab initio modelling (Zhang et al. 2003). The proteinconformation in TASSER is represented by a trace of C αatoms and side chain centresof mass, and the reassembly process is conducted by parallel Monte Carlo simulations(Zhang et al. 2002). The energy terms of TASSER include information aboutpredicted secondary structure propensities, backbone hydrogen bonds, a variety ofshort- and long-range correlations and hydrophobic energy based on the structural