Secondary Structure Assigment
Sample LINUS Run Files
Description of LINUS
LINUS (Local Independently Nucleated Units of Structure) is a program
to simulate protein folding. At its core LINUS is a Metropolis Monte
Carlo procedure. As with any molecular simulation program, at least 3
decisions have to be made.
- Representation of the Protein Structure
- The procedure for exploring conformation space
- The energy function to use.
Representation of the Protein
LINUS represents a protein by including all it's heavy atoms (i.e.,
non-hydrogen atoms). No hydrogens of any kind, polar or non-polar,
are included. A structure suitable for simulation with LINUS can
be generated from a sequence file or a Brookhaven PDB format file
using programs included in the LINUS
Exploring Conformation Space
To explore conformational space, LINUS uses a move set. The moves in
LINUS operate on contiguous 3 residue segments. Four different
types of moves are defined.
Details of the torsion angles for each of the individual moves
are available by following the Move Set link in the side bar.
- α-helix move
- β-strand move
- β-turn move
- coil move
The choice of a 3 residue segment was arrived at by recognizing that
setting 3 consecutive residues to an α-helical conformation
guarantees the formation of one helical hydrogen bond - thus
effective abolishing the helix initiation factor in traditional
The LINUS energy function is more appropriately referred to as a
scoring function. Traditionally energy functions fall in one of
two classes - molecular mechanics based force fields and knowledge
potentials derived from analysis of experimentally known protein
structures. The LINUS scoring function is based on generally known
characteristics of protein structures. Thus, it is known that in
LINUS makes qualitative use of these observations in its scoring
functions. The four components of the scoring function are:
- the backbone peptide groups participate extensively in
inter-residue hydrogen bonding
- the interior of the protein is enriched in non-polar groups
In addition to the generic hydrogen bond term it is possible to check for
the absence of hydrogen bond satisfaction. If a backbone N or O is not
hydrogen bonded intramolecularly or accessible to solvent water,
a penalty is assessed.
- Hard Sphere Repulsion - no two atoms can be at the same place
at the same time
- A contact energy term that rewards bringing hydrophobic residues
- A hydrogen bond term that rewards the presence of hydrogen bonds
between backbone atoms and also between backbone donors and
- A torsion term. This term rewards glycine and asparagine if the
φ value is positive and penalizes other residues if they adopt
a positive φ value.
Finally, this version of LINUS includes a function to estimate the solvation
energy of a protein conformation using the Conditional Accessible Surface
Area (CHASA) algorithm described by Fleming and Rose (2005).