Molecular Modelling SYBYL

Figure 12. Difference of chemical conformations of ephedrine (5) and pseudoephedrine ( ) and distance between hydrogen and nitrogen measured by molecular modeling (Sybyl 6.5, Tripos).

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. 

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

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

Academia has been rich in producing theoretical computational methodology that underpins molecular modeling. The following software arose from universities or private and publicly funded institutes AMBER [10], INSIGHT [11,12], CHARMM [13], SYBYL [14], GRID [15], DOCK [16] and HINT (Hydropathic INTeractions) [39]. All except AMBER were commercialized. 

All of these programs are available for Unix operating system. Most of the Windows versions are incorporated into commercial molecular modeling packages such as MM in Chem3D of CambridgeSoft (http //www.camsoft.com), AMBER and CHARMm in HyperChem of HyperCube (http //www.hyper.com), and SYBYL... 

Figure 1 Molecular model of a 12-base pair duplex of canonical B-form DNA. The two 12-mer strands that intertwine to form the duplex are colored separately (black and gray). Nucleic acid base pairs are stacked perpendicular to the helical axis at 3.4-A intervals (center-to-center distance), and the duplex helix repeats its spiral structure every 10 base pairs. (Figure provided by Dr. Carolyn Kanagy using the Sybyl Version 6.3 molecular modeling program from Tripos, Inc. and standard B-form DNA substructures.)...

Quantitative structure-activity/pharmacokinetic relationships (QSAR/ QSPKR) for a series of synthesized DHPs and pyridines as Pgp (type I (100) II (101)) inhibitors was generated by 3D molecular modelling using SYBYL and KowWin programs. A multivariate statistical technique, partial least square (PLS) regression, was applied to derive a QSAR model for Pgp inhibition and QSPKR models. Cross-validation using the leave-one-out method was performed to evaluate the predictive performance of models. For Pgp reversal, the model obtained by PLS could account for most of the variation in Pgp inhibition (R2 = 0.76) with fair predictive performance (Q2 = 0.62). Nine structurally related 1,4-DHPs drugs were used for QSPKR analysis. The models could explain the majority of the variation in clearance (R2 = 0.90), and cross-validation confirmed the prediction ability (Q2 = 0.69) [ 129]. 

Many of the aforementioned features are combined in integrated molecular modeling software such as SYBYL, Chem-X, COSMIC,80 Quanta and CHARMm, BIOGRAF, Insight and Discover, Chemlab, and MOLIDEA. These packages are available on a variety of hardware platforms ranging from personal computers (PCs) to mainframe computers. 

Molecular modeling with an AMBER-like and MM2 force fields. Batch conformational searching with BAKMDL. Interfaces to AMPAC, MacroModel, GAUSSIAN86, SYBYL, PCMODEL, CHEM-3D. VAX. 

Sybyl Molecular Modeling System (version 6.9.2) Tripos Inc. St. Louis MO. 

The SYBYL molecular modeling package is known for having the comparative molecular field analysis method for finding three-dimensional QSAR. 2 CJACS hits for CoMFA (Comparative Molecular Field Analysis) are plotted in Figure 20. CoMFA was mentioned in the CJACS database 9% as often as SYBYL, indicating that SYBYL is being used for many functions other than CoMFA. 

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