Abstract: In particular, in alternative embodiments, the invention provides pharmaceutical compounds and formulations comprising a family of epoxyketone compounds, which include racemic mixtures or racemates, isomers, stereoisomers, diastereoisomers, derivatives and analogs, and methods for making and using them. In alternative embodiments, pharmaceutical compositions and formulations of the invention are administered to an individual in need thereof in an amount sufficient to treat, prevent, reverse and/or ameliorate an infection, disease or condition that can be ameliorated, treated, prevented or reversed by partially or completely inhibiting a chymotrypsin-like protease or a proteasome activity, including e.g.

Abstract: In particular, in alternative embodiments, the invention provides pharmaceutical compounds and formulations comprising a family of epoxyketone compounds, which include racemic mixtures or racemates, isomers, stereoisomers, diastereoisomers, derivatives and analogs, and methods for making and using them. In alternative embodiments, pharmaceutical compositions and formulations of the invention are administered to an individual in need thereof in an amount sufficient to treat, prevent, reverse and/or ameliorate an infection, disease or condition that can be ameliorated, treated, prevented or reversed by partially or completely inhibiting a chymotrypsin-like protease or a proteasome activity, including e.g.

Abstract: The present invention provides a method of predicting the mutual affinity of two molecules for each other in solution, by computing the configuration integrals of the free molecules and their bound complex as sums over local energy wells. The invention makes accurate calculations computationally tractable for a range of molecular systems by several means, including restraining the conformations of selected molecular components, and using a single conformation representative of an energy well to correct an efficient but less accurate energy model toward a slower but more accurate model.

Abstract: The present invention provides a method of predicting the mutual affinity of two molecules for each other in solution, by computing the configuration integrals of the free molecules and their bound complex as sums over local energy wells. The invention makes accurate calculations computationally tractable for a range of molecular systems by several means, including restraining the conformations of selected molecular components, and using a single conformation representative of an energy well to correct an efficient but less accurate energy model toward a slower but more accurate model.

Abstract: The present invention provides a method of carrying out a molecular modeling calculation and displaying the results thereof through a task-oriented user interface. The overall computational task is divided into subtasks, each of which is outfitted with a tailored graphical user interface. In a preferred implementation, the subtask user interfaces are accessed via tab icons whose layout reflects the normal order of carrying out the subtasks, and downstream subtask user-interfaces are not activated until the information they require is available from upstream subtasks. The invention also provides software that allows the user to view the setup and results of a calculation, but does not provide computational capabilities. The invention is applicable to a wide range of computational tasks.

Abstract: The present invention addresses the need for a fast, accurate and broadly applicable method of computing accurate partial atomic charges in the context of molecular calculations. The method uses the electronegativity equalization approach and is parameterized to reproduce ab initio molecular electrostatic potentials. It uses a new algorithm to ensure correct treatment of molecules having multiple resonance forms that contribute significantly to the electronic structure. The method will be useful in a variety of computational chemistry applications, including structure-based drug design, and the algorithm for identifying alternate resonance forms of molecules has additional applications in molecular modeling and chemical informatics.