Structure Prediction of Loops with Fixed and Flexible Stems

摘要: The prediction of loop structures is considered one the main challenges in protein folding problem. Regardless dependence overall algorithm on data bank, flexibility regions dictates need for special attention to their structures. In this article, we present algorithms structure with fixed stem and flexible geometry. geometry problem, only secondary three residues either side known. also Initial are generated using a probability database torsion angle dynamics Three rotamer optimization introduced alleviate steric clashes between backbone chain rotamers. optimized by energy minimization an all atom force field. clustered traveling salesman problem based clustering algorithm. densest clusters then utilized refine dihedral bounds amino acids loop. entire procedure carried out number iterations, leading improved refined bounds. presented article has been tested 3190 loops from PDBSelect25 set targets recently concluded CASP9 community-wide experiment.