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.