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Cheminformatic tools help researchers extract
usable information from the volumes of data
generated by high-throughput and combinatorial
technologies that characterize modern research
methods. These tools address the need to
facilitate, store, and explore the chemical and
biological data that is key to the success of drug
discovery programs. The connection information
described by bonds forms the fundamentals of
chemical synthesis and legality. OEChem is the
foundation layer for all of OpenEye software, as
well as being a product in of itself.
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OEChem-
cheminformatics and 3D molecular data
handling
A cheminformatics
tool for modelers. Handles many file
formats as flawlessly as any system on
earth, allows complete chemical handling,
transformation, searching, perception and
normalization. Fast, C++ based with Python
and Java wrappers, OEChem is the OpenEye
infrastructure built to encompass all of
our lofty goals (and those of others, such
as the PubChem project).
Seascape Scientific Partner:OpenEye
Scientific Software, New Mexico
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OMEGA-
systematic high-throughput conformer
generation, including 1D or 2D to 3D
structure generation
The bridgehead
between 2D representations and 3D, OMEGA
is the best conformation generator
available. Equally proficient from a 2D
format (SMILES, SDF) or a 3D form, OMEGA
can rapidly evaluate all energetically
feasible structures and return
conformations likely to be bioactive (99%
accurate to within 2.0 Angstroms in an
independent test).
Seascape Scientific Partner:OpenEye
Scientific Software, New Mexico
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FILTER-
molecular screening and selection based on
physical property or functional
group
Need to evaluate
properties for a large set of compounds?
Need to weed out molecules with
undesirable properties from a corporate or
vendor collection? FILTER is designed
around OEChem to rapidly triage chemical
collections based on user supplied
information and preferences.
Seascape Scientific Partner:OpenEye
Scientific Software, New Mexico
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SMACK-
molecular databases query converter and
optimizer (SMARTS and MDL)
Search languages
are designed for ease of expression, not
efficiency. SMACK used proprietary
algorithms to rewrite queries, such as
SMARTS or SLN, into forms that may be more
readily de constructed by search
algorithms found in typical database
chemical cartridges.
Seascape Scientific Partner:OpenEye
Scientific Software, New Mexico
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Lexichem-
state-of-the-art compound name and
structure interconversion
Ogham- elegant
2D structure rendering of
compounds
Applications and
toolkits for the parsing of chemical names
and the depiction of chemical structures.
Lexichem will take structural descriptions
and produce IUPAC names and other
variations, and then will take names and
produce structures. Ogham will produce 2D
diagrams from many formats, either in
pictorial format or coordinate
descriptions.
Seascape Scientific Partner:OpenEye
Scientific Software, New Mexico
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VIDA II -
molecular visualization and data analysis
on very large datasets
Many of OpenEye
tools either generate or sift through vast
quantities of 3D ligand information, and
as such VIDA II is the best program
available for large scale visualization.
VIDA II can handle small lists of
molecules or corporate collections and can
view them as multi-pane 3D, 2D depictions,
SMILES strings, spreadsheet entries, html
forms, graphs and drill-down lists. It can
view them in the context of proteins or
other small molecules, as simple line
models or photo-realistic balls and
sticks. With a python core VIDA II is
easily scriptable and can be tailored to
many end-uses. Works, naturally, on many
platforms.
Seascape Scientific Partner:OpenEye
Scientific Software, New Mexico
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