EFFECTIVE OPTIMIZATION ALGORITHMS FOR FRAGMENT-ASSEMBLY BASED PROTEIN STRUCTURE PREDICTION

Effective Optimization Algorithms for Fragment-Assembly Based protein Structure Prediction

Despite recent developments in protein structure prediction, an accurate new fold prediction algorithm remains elusive. One of the challenges facing current techniques is the size and complexity of the space containing possible structures for a query sequence. Traditionally, to explore this space fragment assembly approaches to new fold prediction have used stochastic optimization techniques. H...

Protein structure prediction based on fragment assembly and parameter optimization.

We propose a novel method for ab-initio prediction of protein tertiary structures based on the fragment assembly and global optimization. Fifteen residue long fragment libraries are constructed using the secondary structure prediction method PREDICT, and fragments in these libraries are assembled to generate full-length chains of a query protein. Tertiary structures of 50 to 100 conformations a...

Protein Loop Prediction by Fragment Assembly

Protein Structure Prediction Based on Fragment Assembly and the β-Strand Pairing Energy Function

We develop an improved version of PROFESY, a novel method for ab-initio prediction of protein tertiary structures based on fragment assembly and global optimization. In contrast to the primitive version presented earlier, where the hydrogen bond was defined only in terms of inter-atom distance, the angle dependence is now correctly incorporated. This new feature allows us to obtain low-energy c...

Constraint based protein fragment assembly

We present a tool that predicts the 3D conformation of a protein, based on Constraint Logic Programming and fragment assembly. The fragments are derived from a database of known protein structures with a preprocessor —also developed for this work— that clusters and classifies the fragments according to their similarity and frequency. The fragments are used as building blocks by the CLP program ...