Phragment: Overview
Phragment is a package that uses a fragment-based protocol for the de novo prediction of protein structures, and can also be used for loop-modelling and model refinement. Phragment is designed to run on Linux-based desktop and server systems.
De novo Modelling
For de novo structure prediction, Phragment uses small fragment building blocks and backbone torsion moves in order to sample the conformational space available to a protein sequence. This space is explored using more than half a dozen different energy functions for efficient discrimination of native structures. Starting from an extended chain, the protocol uses simulated annealing to evaluate fragment insertions, strand shears and torsion angle changes.
Loop Modelling
Phragment can rapidly model short loops (2-15 residues) using our loop database, or larger loops through de novo modelling. When a model containing a chain break is built using Phyre-Lite or the Phyre-Server, the loop database is searched using a combination of stem geometry and sequence-profile comparisons. Remaining spatial gaps are sealed using the Cyclic Coordinate Descent (CCD) loop closure algorithm. For large models with many gaps, loops are constructed for each gap and final models are refined using simulated annealing.
