Computational Quantum Mechanical Biological Framework in Conjunction with the Protein Data Bank

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Biological systems are integrated complex assemblies of macromolecules that use chemical energy to sustain life. As such, their properties area function of their physicochemical parameters such as solubility, lipophilicity, electronic effects, ionization, and stereochemistry, that have profound influence on the chemistry and biochemistry of the complex.This project develops a computational platform that integrates 1. physically-based computational and analytical modeling using QM techniques, 2. experimental databases, 3. computational analysis tools, and 4. visualization/manipulation interfaces, in order to create a transparent and common interface for the use of these now relatively disparate set of tools. This infrastructure will provide a database and integrate associated tools that allows the user to focus on the principles of stereochemistry, chemical synthesis, computational structure prediction, and physical analysis as applied to molecular recognition, biomolecular conformational analysis, and supramolecular chemistry. The end result will impact biologists and biochemists working in areas such as bioorganic chemistry, medicinal chemistry, enzyme structure and function, and nucleic acid recognition.