MacroModel structures

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. 

MacroModel (we tested Version 6.5) is a powerful molecular mechanics program. The program can be run from either its graphic interface or an ASCII command file. The command file structure allows very complex simulations to be performed. The XCluster utility permits the analysis and filtering of a large number of structures, such as Monte Carlo or dynamics trajectories. The documentation is very thorough. 

Fig. I. (Left) Numbering of vinblastine-type alkaloids in this chapter according to the biogenetic scheme of LeMen and Taylor (134), with equivalent atoms in all synthetic intermediates equally labeled. (Right) Approximation of computer-generated, energy-minimized structure, obtained with the Clark Still MACROMODEL program.

We approached the problem of establishing a structure of the "random coil" conformation by first establishing the limits of the present computational model for a known polymeric structure, the a-helix. Coordinates, created by program MacroModel [22] for the carbonyl groups of a-helical oligomers were used, along with published and experimental dipole transition moments, to compute the VCD and absorption spectra of the a-helical conformer. We found that VCD spectra, independent of chain length, can be calculated for octamers, and that the choice of side chain residues is immaterial for the computed spectra. Both calculated and experimental data were normalized to one residue, to permit a comparison between computed and observed spectra. 

Outputs molecule structure files in formats readable by MM2, MM3, MOPAC, AMPAC, MacroModel, and other programs. XDRAW for displaying input and output of MOPAC. BOLTZMANN for conformer populations. VAX, UNIX, and DOS versions. 

The structure of daphmanidin B (67), C25H36NO6, was elucidated by 2D NM R data to possess a l-azabicydo[5.2.2]undecane moiety, like daphnezomines F and G [46]. The relative stereochemistry was deduced from NOFSY correlations. The conformation of the unit (C-2-C-5, C-18 to C-2, C-19, and N) in the l-azabicyclo[5.2.2]undecane moiety, with a twist-chair form as shown in Figure 18.16, was consistent with the results of a conformational search using MMFF force field [60] implemented in the Macromodel program [59]. 

Programs of Dr. Paul A. Bartlett to convert Cambridge Structural Database to one with bond vectors and to search the latter for specified vector relationships. UNIX workstations. TRIAD database of more than 400,000 energy-minimized tricyclic structures for automated design and ILIAD database of more than 100,000 energy-minimized linking structures in MacroModel, CAVEAT, MDL, SYBYL, and PDB formats. Silicon Graphics, IBM RS/6000, and Sun. 

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. 

The X-ray crystallographic structure of the ternary complex, HLADH-NADH-dimethyl sulfoxide, DMSO, has been determined to 2.9 The crystallographic co-ordinates available from the Brookhaven protein data bank were entered into MACROMODEL and the amino acid residues surrounding the active site identified. Using MACROMODEL and ENZYME the substrate binding domain of HLADH was mapped as a cubic section model. The model obtained from this approach were compared with model col 3 obtained by substrate surrogate overlay. 

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... 

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