Structure Determination and Molecular Modeling Software
The following software packages are available from the bioinformatics
core facility:
- Modeller 7v7 is used for homology or comparative modeling
of protein three-dimensional structures (1). The user provides an
alignment of a sequence to be modeled with known related structures and
MODELLER automatically calculates a model containing all non-hydrogen
atoms. MODELLER implements comparative protein structure modeling
by satisfaction of spatial restraints (2, 3), and can perform many
additional tasks, including de novo modeling of loops in protein
structures, optimization of various models of protein structure with
respect to a flexibly defined objective function, multiple alignment of
protein sequences and/or structures, clustering, searching of sequence
databases, comparison of protein structures, etc. Modeller6v2 is a terminal
based program installed on the bioinformatics server. To run Modeller6v2, you
need to secure-shell into bioinf.uthscsa.edu and open an X-terminal in your
home account and type: "mod "
- Insight II (version 2000.1) is a comprehensive
graphic molecular modeling program. In conjunction with molecular
mechanics/dynamics programs such as Discover or CHARMm, you can use
the Insight II program to build and manipulate virtually any class of
molecule or molecular system. In conjunction with other Accelrys products,
you can study molecular properties. The InsightII package is installed on
the SGI O2 in room 420D. It needs to be run from the console. The computer
can be borrowed for lab projects or used in room 420D. To use it,
please schedule with Borries Demeler (567-6592). You start the program by
logging in as user "insight" (no password required) and then open a Unix
shell. Enter the command "insightII" to start the program.
- SnB (Shake and Bake) is a computer program based on Shake-and-Bake,
a dual-space direct-methods procedure for determining crystal structures
from X-ray diffraction data. This program has been used in a routine
fashion to solve difficult structures, containing as many as 1000 unique
non-H atoms, that could not be solved by traditional reciprocal-space
routines based on the tangent formula alone. Recently, SnB has also
been used to determine the anomalously scattering substructures of
selenomethionyl-substituted proteins containing as many as 160 Se
sites. Generally, non-substructure applications require that diffraction
data be measured to 1.1Å resolution or higher although some structures
having several moderately heavy atoms (e.g. S or Cl) have been solved
at 1.4Å. SAS or SIR substructure applications routinely use 3Å data and
have been successful at a resolution as low as 4Å. Shake and Bake
is installed on our Linux cluster for faster execution. For
assistance with this software package please contact Alex Taylor (567-8702).
- Hydro is a suite of programs for the calculation of
sedimentation and diffusion coefficients, rotational relaxation times
and intrinsic viscosities of rigid macromolecules of arbitrary shape that
are represented by bead models. The software is comprised of 5 different
modules which can be started from the command line from an X-terminal by
issuing one of the following commands: hydro5alnx.exe, hydropix5alnx.exe,
hydrosub5alnx.exe, hydronmr5alnx.exe, or hydropro5alnx.exe. Each
model is described in detail in the PDF documentation files listed
below. For assistance with this software package please contact Borries Demeler (567-6592)
Copyright Borries Demeler
(demeler@biochem.uthscsa.edu)