Sausage: protein threading with flexible force fields

Abstract

Sausage is a protein sequence threading program, but with remarkable run-time flexibility. Using different scripts, it can calculate protein sequence-structure alignments, search structure libraries, swap force fields, create models from alignments, convert file formats and analyse results. There are several different force fields which might be classed as knowledge-based although they do not rely on Boltzmann statistics. Different force fields are used for alignment calculations and subsequent ranking of calculated models. Availability: Freely available to academics at ftp://ftp.rsc.anu.edu.au/pub/torda/sausage/README. Contact: Andrew.Torda@anu.edu.au.