Molecular Modelling MACROMODEL

MacroModel V3.5X (1992) Interactive molecular modeling system. Department of... 

Some results on the molecular modeling of N,N -di-methylxYlaramide (1) and IV lV -dihexYlxylaramide (2) using MacroModel V.2 are presented. Nine minimized conformers were considered and their populations calculated. Average 2 3 3 4 were then calculated and those values... 

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. 

Figure 7 Yearly number of publications in the CJACS file mentioning three other molecular modeling programs. CDL is Chemical Design Ltd. The search queries for the curves were (1) macromodel, (2) pcmodel or serena, (3) chemx or chem(w)x or chemical(w)design(w)ltd or chemical(w)design(w)limited, (4) serena, and (5) chemi-cal(w)design(w)ltd or chemical(w)design(w)limited.

The goal of the present study was to develop a computer-based cubic section model of the substrate binding domain of HLADH. It was considered that the Jones cubic section model could be refined by use of computer assisted substrate overlay in combination with kinetic data on a wide variety of substrates. As in the Jones approach we used the alcohol products as the surrogate substrate structures. Thus, we determined the low energy conformation of alcohols produced from ketones that have been reported to be reduced by HLADH and for which comparative kinetic data vs cyclohexanol could be calculated. As well, we determined the preferred conformations of all alcohols that would have been produced from ketones subjected to but failing to undergo HLADH reduction. These calculations utilised molecular mechanics (MACROMODEL) and yielded accurate co-ordinates for ali atoms in each alcohol. Where enantiomeric or stereoisomeric alcohols were produced or capable of production, the co-ordinates of each were calculated. 

Comparison of the X-ray based cubic section model with the substrate surrogate derived cubic section model gave a view of the amino acid residues around the substrate binding domain (Figure 21). Forbidden and boundary regions defined by the substrate surrogate overlay method are near the side chains amino acid residues. Substrate interactions with surface of the amino acid residues could be estimated by molecular mechanics (MACROMODEL). 

Recently, we proposed a new bioactive conformation of paclitaxel, RKDOR-Taxol [50], based on (i) the 19F-13C distances obtained by the REDOR experiment [49], (ii) the photoaffinity labeling of microtubules [51], (iii) the crystal structure (PDB code 1TUB) of the Zn2+-stabilized aP-tubulin dimer model determined by cryo-electron microscopy (cryo-EM) [52], and (iv) molecular modeling (Monte Carlo Macromodel) [50], In this computational biology analysis, we first docked a paclitaxel-photoaffinity label molecule to the position identified by our photoaffinity labeling study and then optimized the... 

Mechanistically, the requisite betaine intermediates [from dioxaphospholanes N and O] adopt either the chair ( C -> 4) or twist-boat ( 85, 82) conformations so that the C-O" and -O-+PPh3 groups can assume the requisite pre-transition state andperiplanar arrangement for suitable displacement of Ph3PO. From the results of molecular modeling studies (/.e., MacroModel II) on both the chair e.g., IC4) and twist-boat betaine e.g., 85, 82) conformers, the small energy differences between them suggest that the twist-boat ( 85 and 82) betaine conformers may also be... 

Molecular modeling calculations were done by the author using the MM2 force field as supplied in Macromodel [152]. 

MODEL Dr. Kosta Steliou Department of Chemistry University of Montreal Montreal, Quebec H3C 3J7, Canada Tel. 514-343-6219, fax 514-343-7586, e-mail steliou vaxrch.cc.umontreal.ca.bitnet 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. 

For those with an interest in true 3-D structures, we have also a number of user-friendly molecular modeling packages available on our system, among them SYBYL, from Tripos Associates, Inc., and Macromodel, from Prof. Clark Still, Columbia University. Both can be accessed via the Versaterm Pro emulation software on the Macintosh, as well as from intermediate and high-performance workstations like the NEC-APC and the Evans and Sutherland PS-300. These specialist packages are maintained by our Drug Design department, who help out users with the specifics of the software. 

W. C. Still, F. Mohamadi, N. G. J. Richards, W. C. Guida, M. Lipton, R. Liskamp, G. Chang, T. Hendrickson, F. DeGunst, and W. Hasel, Primer to MacroModel Interactive Molecular Modeling System. Department of Chemistry, Columbia University, New York, New York, 1989. 

MacroModel V3.5X, Interactive Molecular Modelling System, Department of Chemistry, Columbia University, New York 1992. 

Mohamadi, F Richards, N. G. J., Guida, W. C Liskamp, R., Lipton, M., Caufield, C., et al. (1990) MacroModel an integrated software systems for modeling organic and bioorganic molecules using molecular mechanics. J. Comput. Chem. 11,440-467. 

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