SYBYL

In Sections 2,.3.1-2.3.4, only the four most popular line notations, Wiswesser (WLN), ROSDAL. SMILES, and Sybyl (SEN), arc discussed. Whereas WLN is now almost obsolete, SMILES is quite an important representation and is widely used (Figure 2-7). 

Chemical structures can be transformed into a language for computer representation via line notations such as ROSDAL, SMILES, Sybyl. 

The PEOE procedure has been incorporated into practically ah molecular modeling packages, e.g., SYBYL of Tripos and Catalyst of Accelrys, because of its high speed and the quality of the charge values obtained. 

The Rekker approach is still used with revised Z/ systems, e.g., in the software program Z/SYBYL [8]. Over recent decades various other substructure-based approaches have been developed that are mostly implemented and available as computer programs. 

Tripos is a force field created at Tripos Inc. for inclusion in the Alchemy and SYBYL programs. It is sometimes called the SYBYL force field. Tripos is... 

Chem3D can read a wide variety of popular chemical structure files, including Gaussian, MacroModel, MDL, MOPAC, PDB, and SYBYL. Two-dimensional structures imported from ChemDraw or ISIS/Draw are automatically converted to three-dimensional structures. The Chem3D native file format contains both the molecular structure and results of computations. Data can be exported in a variety of chemical-structure formats and graphics files. 

All molecular modeling studies were performed with the multifaceted molecular modeling software package SYBYL (Tripos Associates Inc., St. Louis, MO). 

Molecular mechanics simulations use the laws of classical physics to predict the structures and properties of molecules. Molecular mechanics methods are available in many computer programs, including MM3, HyperChem, Quanta, Sybyl, and Alchemy. There are many different molecular mechanics methods. Each one is characterized by its particular/orce eW. A force field has these components ... 

SYBYL molecular modeling software. Tripos Inc., St Louis, MO, USA, http //WWW. tripos.com. 

XLOGP, version 2.0, is written in C-h-. The program reads the query compound (represented in SYBYL/MOL2 format), performs atom classification, detects correction factors, and then calculates the log P value. Due to its simple methodology the program is quite fast. It can process about 100 medium-sized compounds per second on an SGI 02/R10000 workstahon. 

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