ABCC Applications Web Page
Welcome to the ABCC Accessible Application Web Page.
From this page, you can get information about our scientific applications and databases. To get more information about any topic, or to run an application, click on any of the mouseover popup menu items on the left-hand side. Program with a tag "Run" is runnable. This site continues to grow, so come back often to check out the many accessible applications available here at the Advanced Biomedical Computing Center (ABCC).
If you have any comments or suggestions, please contact us Help link
Molecular Visualization(1)
3DNA
3DNA is a comprehensive software package for the analysis and
rebuilding of nucleic acid structures. It contains schemes for
calculating local base-pair, step, and helical parameters, and exact
rebuilding of a structure based on these parameters. The rebuilding
routines offer Calladine-Drew style schematic visual models of DNA
as well as full atomic models with sugar-phosphate backbone.
Website: Click Here
Amber
AMBER-Assisted Model Building with Energy Refinement
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual program carries this name, but the various parts work reasonably well together, and
provide a powerful framework for many common calculations.
The term amber is also sometimes used to refer to the empirical force fields that are implemented in AMBER. It should be recognized that the code and the force fields are separate: several other computer packages have implemented the amber force fields, and other force fields can be implemented with the amber program. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement.
Website: Click Here
AutDockTools
AutoDockTools (ADT) is a GUI to prepare, setup and analyze
AutoDock runs. As a standalone, ADT can also do several useful
things such as reading a file (PDB, Sybyl mol2, AutoDock formatted
files ), adding Hs (essential and all), assigning charges
(Gasteiger or Kollman United Atom) etc.
Please quote the following references with ADT results
Sanner, M.F., Spehner, J. -C., and Olson A.J. (1996)
Reduced Surface: an efficient way to compute molecular
surfaces. Biopolymers, Vol. 38 (3), 305-320
Stride: Protein secondary structure assignment from
---------------------------------------------------
atomic coordinates:
-------------------
Frishman, D and Argos, P. (1995) Knowledge-based secondary
structure assignment. Proteins: Structure, function and genetics,
23, 566-579.
Fast Isocontour Library:
------------------------
Copyright @2001 (unpublished work)
The University of Texas at Austin
Email: (ccv@ticam.utexas.edu)
Website: Click Here
Drawna
DRAWNA is a program devoted to fast rendering of 3-D lighted, solid
models of nucleic acids. It allows the user to choose between
several kinds of representation (wire, CPK, balls & sticks, ribbons
& rods) through a Motif control panel. Drawna reads standard *.pdb
files, and may associate to each coordinate file one or several
H-bond file (*.hbd) or parameter file (*.prm).
Website: Click Here
ESPript
ESPript generates a PostScript file of aligned sequences with
graphical enhancements. Its main input is an ascii file of
pre-aligned sequences. Optional files allow further rendering. The
program calculates a similarity score for each residue of the
aligned sequences.
The output shows:
Secondary Structures
Aligned sequences
Similarities
Consensus
Accessibility
Hydropathy
User-supplied markers
Intermolecular contacts
In addition, similarity score can be written in the bfactor column
of a pdb file, to enable direct display of highly conserved areas.
Website: Click Here
gOpenMol
gOpenMol can be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials from programs like the Gaussian, PC GAMESS and Jaguar.
Website: Click Here
GRASP
GRASP is a molecular visualization and analysis program. It is
particularly useful for the display and manipulation of the
surfaces of molecules and their electrostatic properties.
Please use the following reference in all articles which
use Grasp
Anthony Nicholls, Kim Sharp and Barry Honig, PROTIENS, Structure,
Function and Genetics, Vol 11, No. 4, 1991, pg 281ff
Website: Click Here
Gromacs
GROMACS is a versatile package to perform molecular dynamics, i.e.
simulate the Newtonian equations of motion for systems with hundreds
to millions of particles.
It is primarily designed for biochemical molecules like proteins and
lipids that have a lot of complicated bonded interactions, but since
GROMACS is extremely fast at calculating the nonbonded interactions
(that usually dominate simulations) many groups are also using it
for research on non-biological systems, e.g. polymers. For more
detailed information on how to use GROMACS, read the on-line manual
available at http://gromacs.org/documentation/
Plesae cite these articles when you publish research using
GROMACS:
1) Berendsen, H.J.C., van der Spoel, D. and van Drunen, R.,
GROMACS: A message-passing parallel molecular dynamics
implementation, Comp. Phys. Comm. 91 (1995), 43-56.
2) Lindahl, E., Hess, B. and van der Spoel, D., GROMACS 3.0:
A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) 306-317.
Website: Click Here
insightII
InsightII molecular modeling program is Accelrys' 3D graphical environment for molecular modeling. Its powerful interface gives you a seamless flow of data between other Accelrys' programs. Use
the Insight II program to create, modify, anipulate, display, and analyze molecular systems and related data.
There are many Accelrys programs/modules that can be accessed from InsightII. Please, consult the documentation for more details.
Website: Click Here
LIGPLOT
LIGPLOT is a program that automatically generates schematic 2D
representations of protein-ligand interactions. The input is a
standard PDB file and the output is a colour or black-and-white
PostScript file which gives a simple, at-a-glance representation of
the hydrogen bonds and hydrophobic contacts between protein and
ligand. The program is completely general and can be used to show
other interactions such as helix-helix interactions, protein-DNA
interactions, etc.
For more examples on using LIGPLOT see
/usr/local/fbscapp/ligplot/manual/examples/
Reference:
Wallace A C, Laskowski R A & Thornton J M (1995). LIGPLOT: A program
to generate schematic diagrams of protein-ligand interactions. Prot.
Eng., 8, 127-134.
Website: Click Here
MDDisplay
MD Display can be used to create animated display of molecular
system from molecular dynamics trajectories. Rotation, clipping,
coloring, translation, and scaling are controlled by the user
through the mouse and keyboard. Stereo, half-bond coloring, and
control of animation speed are also available.
Website: Click Here
MidasPlus
MidasPlus is an advanced molecular modeling system developed by the
Computer Graphics Laboratory (CGL) at the University of California,
San Francisco. The system is used daily in university-level research
programs in order to display and manipulate macromolecules such as
proteins and nucleic acids. Ancillary programs allow for such
features as computation of molecular surfaces and electrostatic
potentials and generation of publication quality space filling
images with multiple light sources and shadows. MidasPlus is
distributed as documented source code to serve as both a starting
point and training tool for others interested in doing their own
software development. To address the needs of our group's
structure-based drug design program, MidasPlus has been developed
with an emphasis on the interactive selection, manipulation and
docking of drugs and receptors. Although quite powerful in this
application, the system is also somewhat specialized in this
respect: it requires three dimensional atomic coordinate
data for the structures being displayed and expects the primary
structure to be based on linear chains of subunits such as amino
acids or nucleic acids. Using MidasPlus for complex inorganic
compounds or large polymers with many cross-links is discouraged.
MidasPlus is now in use in nearly 400 other laboratories.
References:
T.E. Ferrin, C.C. Huang, L.E. Jarvis, and R. Langridge, ``The MIDAS
Display System,'' J. Mol. Graphics, 6(1):13-27,36-37, 1988.
T.E. Ferrin, G.S. Couch, C.C. Huang, E.F. Pettersen, and R.
Langridge, ``An Affordable Approach to Interactive Desktop Molecular
Modeling,'' J. Mol. Graphics, 9(1):27-32,37-38, 1991.
C.C. Huang, E.F. Pettersen, T.E. Klein, T.E. Ferrin and R.
Langridge, ``Conic: A Fast Renderer for Space-Filling Molecules with
Shadows,'' J. Mol. Graphics, 9(4):230-236, 1991.
G.S. Couch, E.F. Pettersen, C.C. Huang and T.E. Ferrin, ``Annotating
PDB Files with Scene Information,'' Journal of Molecular Graphics
13(3):153-158, 1995.
Website: Click Here
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