Model building molecular mechanics

Tel. 714-955-2120, fax 714-955-2118, e-mail support wavefun.com Model building, molecular mechanics, and ab initio (Hartree-Fock, Moller-Plesset, direct HF) and semiempirical (MNDO, AMI, PM3) molecular orbital calculations. Graphical front-end and postprocessor of the output. Electron density and electrostatic plots. Interface to Gaussian 92. Cray, Convex, DEC, HP, IBM, and Silicon Graphics versions. 

Tel. 617-873-2669, e-mail prophet-info bbn.com Molecular building, molecular mechanics, simulations, and display. Statistical and mathematical modeling and display. Sequence analysis. Structural and sequence database retrieval. UNIX workstations, such as Sun, VAX (Ultrix), DECstations, and Macintosh Ilfx (A/UX). 

Assisted model building with energy refinement (AMBER) is the name of both a force field and a molecular mechanics program. It was parameterized specifically for proteins and nucleic acids. AMBER uses only five bonding and nonbonding terms along with a sophisticated electrostatic treatment. No cross terms are included. Results are very good for proteins and nucleic acids, but can be somewhat erratic for other systems. 

AMBER (assisted model building with energy refinement) a molecular mechanics force field... 

The great generality of thermodynamics is a consequence of its minimal use of specific and detailed models on the other hand, it is the absence of such models that prevents thermodynamics from providing insight into molecular mechanisms. The combination of detailed models with the concepts of thermodynamics is called the extrathermodynamic approach. Because it involves model building, the technique lacks the rigor of thermodynamics, but it can provide information not otherwise accessible. Extrathermodynamic relationships often take the form of correlations among rates and equilibria, and the models used to account for these... 

This extension in the laboratory can be seen as the fantastic hypothesis testing application of molecular modeling. It is rare to find a chemical problem where there are not at least a few theories of the molecular mechanism involved. How many times has each of us heard steric affect or hydrogen bonding invoked as the explanation of a variety of experimental observations made at the bench level How useful would it be to be able to actually build accurate, quantitative models to investigate such ideas ... 

Detailed three-dimensional models of P-gp-substrate complexes representing the various steps of the catalytic cycle would be significantly helpful in elucidating the molecular mechanism for substrate binding and release. The relatively poor 3D structural information available [14—16] and the complex mechanism for compounds undergoing P-gp-compound interactions explain why only a few groups have attempted to build and study 3D homology models for P-gp [56,58,60,70]. 

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