AMBER refers to two things: a molecular mechanical
force field for the simulation of biomolecules (which is in general use
in a variety of simulation programs); and a package of molecular simulation
programs which includes source code and demos.
DOCK
DOCK addresses the problem of "docking"
molecules to each other. It explores ways in which two molecules, such
as a drug and an enzyme or protein receptor, might fit together. Compounds
which dock to each other well, like pieces of a three-dimensional jigsaw
puzzle, have the potential to bind. So, why is it important to able to
identify small molecules which may bind to a target macromolecule? A compound
which binds to a biological macromolecule may inhibit its function, and
thus act as a drug.
CombiBUILD
: CombiBUILD is a structure-based drug design program created to
aid the design of combinatorial libraries.
NMR
Analysis Programs
CORMA
corma (COmplete Relaxation Matrix Analysis)
is a FORTRAN program for calculating the dipole-dipole relaxation matrix
for a system of protons and converting that to intensities expected for
a 2DNOE experiment. Programs for structure elucidation by NMR.
The mardigras and corma programs are two
separate programs for structure elucidation by nmr. newhyd prepares a pdb
file for input to corma.in. If the user has the coordinates in the PDB
format for heavy atoms but not protons, it supplies the missing protons
and their coordinates; it is a stand alone program. corma.in prepares the
output pdb file from newhyd for input to mardigras or corma. mardigras
uses the output pdb file from corma.in for the iterative relaxation matrix
calculation.
MARDIGRAS
mardigras (Matrix Analysis of Relaxation
for DIscerning the Geometry of an Aqueous Structure) is a FORTRAN program
for calculating proton-proton distances from cross-peak intensities measured
from a 2D NOE experiment.
SPARKY/Striker
Sparky is a graphical NMR assignment and
integration program for proteins, nucleic acids, and other polymers. For
more information about what Sparky does look at the introduction in the
manual. If you want to print the manual there is a Postscript version with
links replaced by page references.
UCSF groups
that distribute software include:
Computer
Graphics Laboratory
Magnetic
Resonance Laboratory
Mass
Spectrometry Facility
X-ray
Crystallography Laboratory
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