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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 Modeling(2)
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
Hint
HINT is a novel empirical molecular modeling system with new
methods for de novo drug design and protein or nucleic acid
structural analysis. The HINT model and algorithms are being
developed by Drs. Glen Kellogg and Donald Abraham of the Medicinal
Chemistry Department at Virginia Common wealth University in
Richmond.
Website: Click Here
catalyst
The Catalyst software provide drug design and discovery capabilities such as:
- the generation of multiple conformations with extensive coverage of conformational space
- pharmacophore-based alignment of molecules
- shape-based three-dimensional database searching
- automated generation of pharmacophore hypotheses based on SAR data
Catalyst also provides provides an integrated environment for database management and querying tasks.
Website: Click Here
cerius2
Cerius2 provides a wealth of tools for applications for life science modeling and simulations. Please, consult www.accelrys.com/cerius2/ for the list of available modules and functionalities.
Website: Click Here
quanta
Quanta is a powerful modeling software for modeling macromolecules and small
organic molecules. For more detailed
information, refer to the documentation
page at http://ncisgi.ncifcrf.gov/accelrys
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
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
MOIL-View
MOIL-View is a program designed to allow the user to view and
analyze molecular structures and molecular dynamics trajectories.
Currently supported file formats:
Coordinates:
CRD: CHARMm format coordinate files
PDB: format used by the Brookhaven Protein Data Bank
AMBER: AMBER restart file format. Coordinates are required while
velocities and box dimensions are not. If box dimensions are
present, they are used for the 'draw box outline' command.
Trajectory:
DCD: format used by the CHARMm and MOIL programs
PATH: higher precision format used by MOIL
AMBER: only formatted AMBER files are allowed (no binary files).
This option is for trajectories that do not include periodic box
information.
AMBER PBC: This option should be used for AMBER trajectories which
contain periodic box information.
Website: Click Here
MSP
The Molecular Surface Package performs computations and
visualizations of molecular surfaces. It consists of three programs:
MSRoll
reads protein data bank format atomic coordinate file
computes a dot surface (similar to that produced by MS)
computes piecewise quartic molecular surface
identifies and characterizes interior cavities
computes molecular areas and volumes
computes a polyhedral surface
MSDraw
renders molecular surface and chemical model
generates polyhedral surface plots with hidden-line elimination
generates contours on a polyhedral molecular surface
MSForm
measures the curvature of a polyhedral molecular surface
computes a solvent-excluded density
computes an interfacial surface between two densities
Website: Click Here
O
O is a macromolecular crystallographic modeling tool. It can be used
to look at macromolecular structures, analyze them, compare them,
modify them and to build them from scratch.
Website: Click Here
PBCAID
PBCAID is to assist the setup process for molecular simulation. It
provides optimization of the dimemsions and orientation of the
periodic boundary cell. It reduces the volume of the periodic cell
by finding the solute rotation that yields the smallest periodic
cell dimentions. Results show that PBCAID can optimize system
volumes by 20 to 70% which leads to substantial computational
savings in the non-bonded pairs calculations.
Website: Click Here
SWISS-MODEL
SWISS-MODEL is a fully automated protein structure homology-modeling
server, accessible via the ExPASy web server, or from the program
DeepView (Swiss Pdb-Viewer). The purpose of this server is to make
Protein Modelling accessible to all biochemists and molecular
biologists World Wide.
Website: Click Here
SYBYL
SYBYL is a general use molecular modeling and visualization package.
It provides essential construction, editing, and visualization tools
for both large and small molecules.
Building and Editing
Molecular structures can be entered from a variety of sources.
SYBYL reads many formats, including MDLi MOL and SD, Cambridge
Structural Database, Protein Data Bank, and SMILES. Direct entry
of structures is also possible using SYBYL's sketcher or 3D
building tools.
Computation
Geometry optimization (minimization) is performed via molecular
mechanics or quantum mechanical (interface to MOPAC) methods.
SYBYL offers a variety of force fields (Tripos, Amber, MM2 and
MMFF94) as well as several options for computing or importing
atomic charges. Several algorithms are available for generating
solvent models. Geometric features such as planes, normals, and
centroids can be defined. Distance, angle, and torsion constraints
for minimization can be keyed to individual atoms or geometric
features.
Molecular Spreadsheet
SYBYL contains built-in tools for analysis of molecular structure,
as well as the interactive Molecular Spreadsheet. The Molecular
Spreadsheet (MSS) organizes the analysis of molecule sets. Rows
represent molecules, and columns contain related metrics such as
molecular weight, topographical data, energies, and biological
activity. Over 60 built-in metrics are available, with others
provided by additional modules.
Visualization
Molecules can be displayed as lines, sticks, ball-and-stick, or
spacefilling spheres. Colors, labels, depth cueing, shading,
stereo view mode, and Z-clipping can be readily changed through
the toolbar. Volume displays, contours, grids, and dotted surfaces
provide the ability to visualize molecular properties. Views can
be annotated with arrows and text, either in 2D or with elements
that rotate and translate with the molecules.
Customization
SYBYL enables custom design methods via the SYBYL Programming
Language (SPL).
Website: Click Here
ViennaRNA
The Vienna RNA packages consists of a few stand alone programs and a
library that you can link your own programs with. The package allows
you to
- predict minimum free energy secondary structures
- calculate the partition function for the ensemble of structures
- calculate suboptimal structures in given energy range
- predict melting curves
- search for sequences folding into a given structure
- compare secondary structures including pairwise alignment.
There is also a set of programs for analysing sequence and distance
data using split decomposition, statistical geometry, and cluster
methods.
The following executables are provided:
RNAfold predict secondary structures
RNAsubopt calulate suboptimal structures in a given energy
range
RNAeval evaluate energy for given sequence and structure
RNAheat calculate melting curves
RNAdistance compare secondary structures
RNApdist compare ensembles of secondary structures
RNAinverse find sequences folding into given structures
AnalyseSeqs analyse sequence data
AnalyseDists analyse distance matrices
RNAplot
Website: Click Here
VMD
VMD is a molecular visualization program for displaying and
animating large biomolecular systems using 3-D graphics. VMD
supports computers running Unix or Windows, is distributed free
of charge, and includes source code.
VMD is designed for the visualization and analysis of biological
systems such as proteins, nucleic acids, lipid bilayer assemblies,
etc. It may be used to view more general molecules, as VMD can
read standard Protein Data Bank (PDB) files and display the
contained structure. VMD provides a wide variety of methods for
rendering and coloring a molecule: simple points and lines, CPK
spheres and cylinders, licorice bonds, backbone tubes and ribbons,
cartoon drawings, and others.
VMD can be used to animate and analyze the trajectory of a
molecular dynamics (MD) simulation. In particular, VMD can
act as a graphical front end for an external MD program by
displaying and animating a molecule undergoing simulation.
The authors request that any published work which utilizes VMD
include the following reference:
Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular
Dynamics" J. Molec. Graphics 1996, 14.1, 33-38.
Website: Click Here
WHAT_CHECK
WHAT_CHECK is a protein verification subset of the program WHAT IF.
Website: Click Here
CambridgeDB
The Cambridge Structural Database is the world repository of small molecule crystal structures
The Cambridge Structural Database (CSD) is the principal product the CSD System, which also comprises software for database access, structure visualisation and data analysis, and structural knowledge bases derived from the CSD.
The CSD records bibliographic, chemical and crystallographic information for organic molecules
and metal-organic compounds whose 3D structures have been determined using X-ray diffraction or neutron diffraction.
Website: Click Here
CAP_2002_DbSearch
Website: Click Here
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