Program Description: |
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).
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Documentation: |
Available in the html format in the directory
/usr/local/fbscapp/sybyl/TriposBookshelf
If you are on the ncifcrf.gov network, the following URL will also work for you
- http://ncisgi.ncifcrf.gov/tripos/. Note, that the "Search the Tripos Bookshelf"
functionality works only with the browser run on ncisgi.ncifcrf.gov.
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