Software available from UCLA-DOE:
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ASP |
Calculation of the hydrophobic folding energy of a
protein, the hydrophobic binding energy, and structural hydrophobic moments.
This code was last updated Nov 30, 1996
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BEND |
Calculates local bending and macroscopic curvature
along a DNA double helix of arbitrarily selected sequence, based on the
user's input table of helix twist, roll and tilt at each of the ten different
sequence steps from one base pair to the next. The input table parameters
can be varied in order to test the relative validity of different DNA bending
models
[Goodsell & Dickerson, 1994].
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CPROF |
Continious Profile method programs. The source code
is implemented as described in
[Zhang & Eisenberg, 1994].
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ERRAT |
Analyzes statistics of interactions between different
atom types to identify regions of protein structures that may be in error
or require adjustment. This is useful during the course of model-building
and crystallographic refinement
[Colovos & Yeates, 1993].
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Rossmann fold detector |
An FAD or NADP binding Rossmann fold detector
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Ezprot |
Ezprot is a library of functions and object-oriented classes which greatly
simplifies computational analysis of the molecular structure and sequence
of proteins. The functions implement many common tasks such as reading
PDB files, calculating surface areas, rotating or moving a structure,
finding specific amino acids in a structure, etc. The functions work
together and allow you to write compact, highly readable source code for
advanced structure/sequence analysis. The interface is simple enough for
graduate students and those just beginning to work in computational
molecular biology. However, it is flexible and powerful enough to assist
advanced research. The library is written in C++ but has a "C-like"
interface. The documentation is extensive and very clear.
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HASSP |
Performs a search for solutions to a Patterson function
using an automated space-group symmetry minimum method.
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HEAVY |
Performs heavy atom refinement using an origin-removed Patterson.
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ION |
Ion site finding program. The program calculates
FFT maps of various functions over a grid covering a molecule. One of the
functions available is essentially the same as Mason Yamashita's ion binding
site function, described in
[Yamashita et al., 1990].
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LATTICE |
This package contains the necessary programs to calculate the average reciprocal unit cell from diffraction data.
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MAXRAD |
Performs an analytical calculation of the radius
of the largest sphere that can contact each atom in a structure (of course
without colliding with any other atoms). The algorithm involves geometric
inversion in a sphere
[Yeates, 1995].
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MOMENT Transmembrane Helix Prediction |
Passes a window over a protein sequence, determines
the average hydrophobicity, alpha and beta helical moments, and classifies
each window as SURface, MULtimeric, MONomeric or other
[Eisenberg et al., 1982;
Eisenberg et al., 1984;
Eisenberg & Wesson, 1990].
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NEWHEL |
Uses atomic coordinates from a DNA or RNA double
helix to calculate local helix parameters such as twist, roll, tilt, rise,
etc., main chain torsion angles, sugar pseudorotation angles, and P-P and
O4'-O4' distances across major and minor grooves
[Dickerson, 1989]
and
[Dickerson, 1989].
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PDB3D |
PDB3D is a high speed 3D molecule rendering applet which has been
designed specifically for viewing
Protein Data Bank (PDB) format molecular structure files within web
pages. As a benchmark, PDB3D can render an alpha carbon trace of a 3000
residue protein at approximately 2 fps and that of a 500 residue protein at
approximately 10 fps when running as interpreted Java within Netscape 2.01
(by Scott M. Le Grand).
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Profile Search
and Verify3D |
x
Profile Search Software
[Bowie et al., 1991;
Luethy et al., 1992].
Commercial users please contact BIOSYM at (619) 458-9990.
Academic users can obtain a free copy of these programs after returning
a signed License form:
([post script] or
[PDF])
and print it on any Postscript printer). Please fill and sign the
last page of the license and fax both pages to (310) 206-3914. The programs
and instructions to run these programs will be sent by e-mail to the address
you print at the bottom of the License form.
If you have more questions, send e-mail to
Ms. Cindy Chau
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RESPAIR |
Calculates residue pair preference profile. The program
package consists of two parts, generation of scoring tables (TABLEPAIR)
and generation of profiles (PROFILEPAIR). Both steps can be carried out
by characterizing residue pairs in three different ways: (a) residue types
(amino acids) as function of distance, (b) (phi,psi) classes as function
of residue types, (c) and secondary structure classes as function of residue
types. You can skip the first step and use the scoring tables provided
by this package. The complete list of PDB files used for generation of
the available scoring tables is given in the file PDB.LIS. The generated
profiles can be used by programs like PROFILESEARCH, PROFILEGAP etc.
(see GCG program package)
[Wilmanns & Eisenberg, 1993].
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SASA |
Calculates the Solvent Accessible Surface Area for the molecule in PDB format
(by Scott M. Le Grand).
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Squash |
An integrated system for macromolecular phase refinement
and extension which combines Sayre's equation, molecular averaging, solvent
flattening and histogram matching. The constraints used in these methods
are the correct local shape of the electron density, equal molecules, solvent
flatness and the correct electron density distribution. These constraints
on electron densities are satisfied simultaneously by solving a system
of non-linear equations by Newton-Raphson method using FFT's
[Main, 1990].
The electron density solution is further filtered by a phase
combination procedure. The non-crystallographic symmetry operations can
be refined by a rotation and translation space search and a least squares
minimization method, thereby reducing the chance of introducing systematic
phase errors during averaging. Some auxiliary routines are also incorporated
into the program, such as Wilson scaling, map handling, etc.
[Zhang, 1993].
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TPlot |
A quick plotting program generating plotted images
via the web. Can generate up to 3 plots. Input data can have upto 7 columns of data.
Use the GD Library;
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html2txt.pl |
Very simple HTML to ASCII text converter (written by Robert Stockton (rgs@cs.cmu.edu).
It is unable to deal with complicated HTML. A more advanced version is to replace this one.
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