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The Protein Folding Problem
Proteins, long strings of amino acids, self-organize spontaneously into unique
three-dimensional structures when introduced to aqueous solvent.
Far from being a random process, protein folding is a series of
energy-directed events called a Pathway. Protein sequences encode somehow the
order of events in folding.
Chris Bystroff, associate professor of biology, uses statistical
models and molecular simulations to understand the pathways of protein
folding. His applications allows users from around
the world to submit sequences and predict the likely folding
initiation sites and structural features.
Notice
- HMMSTR/I-sites/Rosetta
HMMSTR is a Hidden Markov Model based on protein STRucture.
Each Markov state in this model represents a position in one
of the I-sites motifs. HMMSTR
can predict local structure (as backbone angles), secondary
structure, and supersecondary structure (edge versus middle
strand, hairpin versus diverging turn). For more, see these
references.
- I-sites Library
I-sites is a library of folding initiation site motif, which
are sequence motifs that correlate with particular local structures
such as beta hairpins and helix caps. I-sites
can be used to predict local structure, or to predict which
parts of a protein are likely to fold early, initiating folding.
For more, see these references.
- PROTEAN
PROTEAN is a program for doing Brownian dynamics of polypeptides
in torsion space using implicit solvent . The current energy
functions are untested, but the equations of motion in torsion
space have been tested, validated and optimized for speed (see
this reference in pdf format). Protean can be used to generate
coordinates from torsion angles, or vice versa. Protean can
also fit a sequence to a template structure. Fortran source
code is provided.
- MASKER
MASKER computes the solvent excluded surface (see Michel
Sanner's site) using Boolean masks. The program is robust
and fast. Try our
server for surface area computation.
Use this server to calculate
the buried surface area in any PDB structure, using MASKER.
Fortran 90 source
code is available. For more, see this
reference in pdf format.
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