Integrated Modeling Package - MPACK Version 1.0
MPACK (Modeling Package) is an integrated protein modeling suite that currently handles comparative and ab initio modeling procedures. The objective of this suite is to systematically bring different steps (or programs) under one roof in order to facilitate rapid model generation with minimal user effort and to create a biological data-flow pipeline for large scale-scale modeling of protein sequences from genomic projects. This integrated suite was created with the geometry extraction program EXDIS that extracts distance and dihedral constraints, specified using protein template for which experimental structure is known. Inside/outside, secondary structure predictions from MASIA and other knowledge based topological constraints can be used directly to convert into suitable distance constraints using TRANSLATE. Geometric constraints generated are directed as input into the distance geometry program DIAMOD that optimally calculates structures by either starting from a random conformation or from approximate models produced by EXDIS. The program also has an option for generating models with disulphide bonds and switches for self-correcting distance geometry procedures when approximate constraints (like constraints from MASIA predictions) are used. The package is robust and efficient in handling situations wherein a user intends to model a target based on multiple template fragments.