SYBYL software

From a procedural standpoint, the start and stop residues of each of the seven helices was first identified by hydropathy analysis by using Kyte-Doolittle19 hydropathy indices. Each of the seven helices was then built individually, essential hydrogens were added, and the peptides were minimized with the Kollman United Atoms force field within the Sybyl software suite (Tripos Associates, Inc.). Typically, steepest descent was used initially as the minimization method (25-50... 

The ligand-based alignments were carried out using the superposition program FlexS [2], and compound 4j as rigid template (in the conformation obtained by the docking) on the one site and the Multifit routine within the SYBYL software and the same template on the other site (Fig. 11.5). 

Leapfrog Is a component of the SYBYL software package (Tripos) and is a second-generation de novo drug discovery program that allows for the evaluation of potential ligand structures... 

R. A. Dammkoehler, S. F. Karasek, E. F. B. Shands, and G. R. Marshall,/. Comput.-Aided Mol. Design, 3,3 (1989). Constrained Search of Conformational Hyperspace. This method is implemented in the RECEPTOR module for the SYBYL software package. Tripos Associates, St. Louis, MO. 

The antimalarial activity of (9) involves its interaction with heme or hemin in the parasitized erythrocyte. Molecular modeling techniques have been used to investigate how the two molecules dock, the one on the other <95MI 620-0l>. The x-ray structures of artemether (23) and hemin have been taken and modeled with the SYBYL software. It is found that, in the optimum interaction, the peroxide bridge lies close to the central iron atom of heme or hemin. It will be seen in Section... 

Two figures, printed directly from SYBYL software, show the windows with parameters used for energy minimization. As a dielectric function and dielectric constant, the default parameters were used (a value of 1 was used for the dielectric constant) as shown in Fig. 5b. The dielectric constant 1 corresponds to vacuum and it adequately represents the binding performed in hydrophobic conditions, favorable for electrostatic interactions. The Gradient termination was used and convergence was reached when the difference in energy between one step and the next was less than 0.001 kcal/mol, achieved within 2000 iterations. The structure of Microcystin-LR obtained (Fig. 6) was utilized for the subsequent computational design. 

Molecular models were generated using Tripos Sybyl software, version 5.4. Hydrogens are not shown. Top left, 20-P-hydroxyecdysone (73), top right. 

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