The LINUS_23 distribution is a suite of programs for exploring conformational ensembles of peptides and proteins.
The core of LINUS is a torsion angle Monte Carlo simulation application that allows a restrained Monte Carlo move set with a simple atomic interaction energy acceptance criterion.
Version 2.3 introduces backbone hydrogens, an expanded hydrophobic contact scoring function, and expanded side chain hydrogen bonding capability and a side chain rotamer library from S. Lovell et al. (PROTEINS 40:389-408, 2000).
The addition of backbone hydrogens has the effect of sterically allowing φ,ψ moves that are described by a standard Ramachandran map.
Several additional flags have been added to allow conformational constraints during simulations.
Inclusion of backbone hydrogens necessitates the addition of a cap on the N-terminus of the polypeptide to facilitate the use of internal coordinates.
An acetyl group (ACE) is therefore included in all structures in version 2.3.
For symmetry a C-terminal cap, N-methyl amide (NME) is also included in all structures in this version of LINUS.
The residue index of ACE is 0 and the residue index of NME is N-1 where N is the total number of residues including the caps.
Click on the LINUS menu item at the left for a more complete description of the program.
Included with the LINUS distribution is a collection of helper programs and utilities for the interconversion, creation and analysis of protein sequences and structural models.
LINUS is written entirely in Python although some routines are also provided as C code.
The C routines will be called if they are compiled but they are not necessary.
For any publication arising from use of the LINUS program suite, a reference should be given as:
Srinivasan R., Rose G.D. LINUS - A Hierarchiacal Procedure to Predict the Fold of a Protein. PROTEINS 22(2): 81-99 JUN, 1995
Other references describing the use of LINUS are given in the reference list.
Copyright (C) 2002 Raj Srinivasan, Patrick Fleming, George Rose
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
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