Abstract: 7-(substituted) derivatives of 7H-pyrrolo[3,2-f]-quinazoline-1,3-diamines, derivative thereof, and methods of using them are provided. The pharmaceutical formulations prepared from the compounds can be used to treat a variety of conditions, which include, but are not limited to bacterial and fungal infections. The compounds can also be used as a sterilizing or disinfecting agent.

Abstract: 7-(substituted) derivatives of 7H-pyrrolo[3,2-f]-quinazoline-1,3-diamines, derivative thereof, and methods of using them are provided. The pharmaceutical formulations prepared from the compounds can be used to treat a variety of conditions, which include, but are not limited to bacterial and fungal infections. The compounds can also be used as a sterilizing or disinfecting agent.

Abstract: A method, computer-readable medium, and system for identifying one or more metabolites associated with a disease, comprising: comparing gene expression data from diseased cells to gene expression data from control cells in order to deduce genes that are differentially-regulated in the diseased cells relative to the control cells; based on enzyme function and pathway data for all human metabolites that utilize the genes that are differentially-regulated in the disease cells, identifying one or more metabolites whose intracellular levels are higher or lower in diseased cells than in control cells, and thereby associating the one or more metabolites with the disease.

Abstract: A method, computer-readable medium, and system for identifying one or more metabolites associated with a disease, comprising: comparing gene expression data from diseased cells to gene expression data from control cells in order to deduce genes that are differentially-regulated in the diseased cells relative to the control cells; based on enzyme function and pathway data for all human metabolites that utilize the genes that are differentially-regulated in the disease cells, identifying one or more metabolites whose intracellular levels are higher or lower in diseased cells than in control cells, and thereby associating the one or more metabolites with the disease.

Abstract: A method, computer-readable medium, and system for identifying compounds from chemical libraries that can be used for the therapeutic treatment of a disease or used as lead compounds in a drug development program. In particular, information from homologous proteins is used to predict, for a target protein, molecular functions that can be used to screen libraries of compounds for individual compounds that are predicted to have high binding affinities for the target protein.

Abstract: The present invention concerns methods and systems for predicting the biological function(s) of proteins. The invention is based on the development of functional site descriptors for discrete protein biological functions. Functional site descriptors are geometric representations of protein functional sites in three-dimensional space, and can also include additional parameters, for example, conformational information. Following their development, one or more functional site descriptors (for one or more different biological functions) are used to probe protein structures to determine if such structures contain the functional sites described by the corresponding functional site descriptors. If so, the protein(s) containing the functional site(s) are predicted to have the corresponding biological function(s).

Abstract: The invention provides a new, efficient method for the assembly of protein tertiary structure from known, loosely encoded secondary structure constraints and sparse information about exact side chain contacts. The method is based on a new method for the reduced modeling of protein structure and dynamics, where the protein is described by representing side chain centers of mass rather than alpha-carbons. The model has implicit, built-in multi-body correlations that simulate short- and long-range packing preferences, hydrogen bonding cooperativity, and a mean force potential describing hydrophobic interactions. Due to the simplicity of the protein representation and definition of the model force field, the Monte Carlo algorithm is at least an order of magnitude faster than previously published Monte Carlo algorithms for three-dimensional structure assembly.

Abstract: Improved methods for generalized comparative modeling are described, as is the application of a preferred embodiment of such methods on the Fischer database of 68 probe-template pairs, a standard benchmark to evaluate threading approaches. Briefly, the invention utilizes ab initio folding (for example, a lattice protein model, SICHO (for “Side Chain Only”) near a template provided by an alignment method, for example, a threading algorithm (e.g., PROSPECTOR). These methods can be readily automated and implemented on whole genome (or proteome) scales.

Abstract: The present invention concerns methods and systems for predicting the biological function(s) of proteins. The invention is based on the development of functional site descriptors for discrete protein biological functions. Functional site descriptors are geometric representations of protein functional sites in three-dimensional space, and can also include additional parameters, for example, conformational information. Following their development, one or more functional site descriptors (for one or more different biological functions) are used to probe protein structures to determine if such structures contain the functional sites described by the corresponding functional site descriptors. If so, the protein(s) containing the functional site(s) are predicted to have the corresponding biological function(s).

Abstract: A general neural network based method and system for identifying peptide binding motifs from limited experimental data. In particular, an artificial neural network (ANN) is trained with peptides with known sequence and function (i.e., binding strength) identified from a phage display library. The ANN is then challenged with unknown peptides, and predicts relative binding motifs. Analysis of the unknown peptides validate the predictive capability of the ANN.

Abstract: A computer system and method are disclosed for determining a protein's tertiary structure from a primary sequence of amino acid residues. The system uses a dynamic Monte Carlo method with Metropolis sampling criterion, and a selected (2,1,0) lattice model, to simulate protein folding during the transition of the protein from an unfolded (denatured) state to its native, folded state. The system generates, for display, a folding trajectory representing successive three-dimensional images of the protein at a level of two Angstrom resolution as it folds to its native conformation. The system permits interaction between all proximate pairs of sidechains of the protein and provides faster processing through the use of the lattice.