Abstract: The invention relates to methods for forming combinatorial libraries. The invention provides methods suitable for the rapid and convenient synthesis of very large combinatorial libraries of small organic molecules. In particular, the invention provides a method for forming combinatorial libraries combining amide bond formation with epoxide opening.

Abstract: A system and method are used to evaluate concavities in a complex surface, such as for determining protein pockets in a protein model.

Abstract: The present invention provides a method for producing a mass-coded combinatorial library comprising a set of compounds having the general formula X(Y)n, where X is a scaffold, each Y is, independently, a peripheral moiety, and n is an integer greater than 1. The method comprises selecting a peripheral moiety precursor subset from a peripheral moiety precursor set. The subset includes a sufficient number of peripheral moiety precursors that at least about 50 distinct combinations of n peripheral moieties derived from the peripheral moiety precursors in the subset exist. The subset of peripheral moiety precursors is selected so that at least about 90% of all possible combinations of n peripheral moieties derived from the subset have a molecular mass sum which is distinct from the molecular mass sums of all of the other combinations of n peripheral moieties. The method further comprises contacting the peripheral moiety precursor subset with a scaffold precursor which has n reactive groups.

Abstract: Methods for forming combinatorial libraries and the libraries produced thereby are provided. According to a preferred aspect of the invention, a plurality of core molecules are reacted with a plurality of different tool molecules to form a library of molecules having non-naturally occurring molecular diversity. The libraries are useful for identifying lead compounds which modulate the functional activity of a biological molecule. Protease inhibitors that have been isolated from the libraries also are disclosed.