Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space.

ABSTRACT:

Background

Various forms of the so-called loop closure problem are crucial to protein structure prediction methods. Given an N- and a C-terminal end, the problem consists of finding a suitable segment of a certain length that bridges the ends seamlessly. In homology modelling, the problem arises in predicting loop regions. In de novo protein structure prediction, the problem is encountered when implementing local moves for Markov Chain Monte Carlo simulations. Most loop closure algorithms keep the bond angles fixed or semi-fixed, and only vary the dihedral angles. This is appropriate for a full-atom protein backbone, since the bond angles can be considered as fixed, while the (phi, psi) dihedral angles are variable. However, many de novo structure prediction methods use protein mod

SUBMITTER: Boomsma W 

PROVIDER: S-EPMC1192790 | biostudies-literature | 2005 Jun

REPOSITORIES: biostudies-literature