Computer
& Sequence Analysis/Bioinformatics
Molecular
Modeling and Graphics
The core
facility maintains the
Discovery Studio molecular
modeling package from
Accelrys in room C5716,
Molecular Visualization Lab.
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Discovery
Studio Standalone
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Discovery Studio
Standalone is a complete
molecular modeling
platform designed for
the independent modeler.
This standalone
environment, powered by
the Pipeline Pilot open
platform includes the
entire infrastructure
needed to design and run
modeling experiments
with Discovery Studio
Science. Easily
visualize, model, and
analyze biological and
chemical data using
tools for sketching
3D
molecules, visualizing
dynamic changes,
3D
graphing and a host of
other functionality. The
standalone installation
can also be connected
into a Pipeline Pilot
Server for easy sharing
of workflows and data.
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Discovery
Studio Visualizer Client
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Discovery Studio
Visualizer Client is a
powerful graphical
interface to access
Discovery Studio
Science. DS Visualizer
Clients can be
inexpensively deployed
and easily maintained
for research teams while
still offering
world-class science.
When deployed with a
Pipeline Pilot Server,
DS Visualizer Client
offers unparalleled
capabilities for sharing
data, workflows, and
computational resources.
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Pipeline
Pilot Server
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Pipeline Pilot makes the
most of your information
through industrial-scale
data flow control and
powerful mining
capabilities. You can
graphically compose data
processing networks,
using hundreds of
different configurable
components for
operations such as data
retrieval, manipulation,
computational filtering,
and display. These
protocols are
automatically captured
as you create them and
you can even publish
them for
enterprise-level
deployment. Your
colleagues have the
option to invoke your
protocols and run them
using their own data
using a simple Web
interface. |
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Discovery
Studio Free Visualizer
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View and share protein
and small-molecule data
in a clear and
consistent way, and in a
wide variety of
industry-standard
formats. This free,
easy-to-use
visualization tool is an
ideal solution for
managers and researchers
who need to collaborate
with modelers, but do
not need access to the
expert-level analysis
tools in Discovery
Studio. |
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DS
Analysis |
Gain new insights into
molecular processes by
using DS Analysis to
animate, graph, and
tabulate results of
CHARMm molecular
dynamics, small molecule
docking, or protein
modeling. Analyze MD
trajectories in an
intuitive, easy-to-use
manner by computing the
Radius of gyration (RGYR),
radial distribution
function, clustering of
trajectories with
ability to select
clusters through a
dendogram plot,
Principle Component
Analysis (PCA), and
Phi-Psi Time series.
Compute RMSD, hydrogen
bonds and close contacts
for thousands of docked
ligand poses in a single
job. Calculate RMSD of
residues/atoms during
the course of a
trajectory; display the
result in a dendrogram
or heat map. Check the
quality of the protein
structure and analyze
regions with
abnormalities using the
‘Protein Health’
toolpanel. Evaluate
model quality based on
the MODELER DOPE
(Discrete Optimized
Protein Energy) energy
function. |
For
information pertaining to
Molecular Modeling and Graphics,
please contact:
David
R. Stanford, Ph.D.
Room C1727
Phone (717) 531-4699
Email
drs19@psu.edu
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