Abstract: Thrombin-inhibiting acylated pyrazole-pyridone compounds of formula (II) are disclosed herein, as well as pharmaceutical compositions, including tablets, that contain acylated pyrazole-pyridone compounds. These compounds are useful for the treatment and prevention of thrombin-related related diseases and disorders. Processes for making tablets containing acylated pyrazole-pyridones are also included.

Abstract: There are provided inter alia multisubstituted aromatic compounds useful for the inhibition of thrombin, which compounds include substituted pyrazolyl or substituted triazolyl. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing a disease or disorder, which disease or disorder is amenable to treatment or prevention by the inhibition of thrombin.

Abstract: There are provided inter alia multisubstituted aromatic compounds useful for the inhibition of thrombin and/or kallikrein, which compounds include substituted pyrazolyl. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing certain diseases or disorders, which diseases or disorders are amenable to treatment or prevention by the inhibition of thrombin and/or kallikrein.

Abstract: There are provided inter alia multisubstituted aromatic compounds useful for the inhibition of kallikrein, which compounds include substituted pyrazolyl or substituted triazolyl. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing certain diseases or disorders, which disease or disorder is amenable to treatment or prevention by the inhibition of kallikrein.

Abstract: There are provided inter alia pyrazolyl-substituted pyridone compounds, which exhibit biological activity, e.g., inhibitory action, against serine proteases, including thrombin and various kallikreins. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing certain diseases or disorders, which disease or disorder is amenable to treatment or prevention by the inhibition of serine proteases, including thrombin and various kallikreins.

Abstract: There are provided inter alia multisubstituted aromatic compounds useful for the inhibition of kallikrein, which compounds include substituted pyrazolyl or substituted triazolyl. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing certain diseases or disorders, which disease or disorder is amenable to treatment or prevention by the inhibition of kallikrein.

Abstract: There are provided inter alia multisubstituted aromatic compounds useful for the inhibition of thrombin, which compounds include substituted pyrazolyl or substituted triazolyl. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing a disease or disorder, which disease or disorder is amenable to treatment or prevention by the inhibition of thrombin.

Abstract: There are provided inter alia multisubstituted aromatic compounds useful for the inhibition of thrombin, which compounds include substituted pyrazolyl. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing a disease or disorder, which disease or disorder is amenable to treatment or prevention by the inhibition of thrombin.

Abstract: There are provided inter alia multisubstituted aromatic compounds useful for the inhibition of kallikrein, which compounds include substituted pyrazolyl or substituted triazolyl. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing certain diseases or disorders, which disease or disorder is amenable to treatment or prevention by the inhibition of kallikrein.

Abstract: There are provided inter alia multisubstituted aromatic compounds useful for the inhibition of thrombin, which compounds include substituted pyrazolyl or substituted triazolyl. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing a disease or disorder, which disease or disorder is amenable to treatment or prevention by the inhibition of thrombin.

Abstract: There are provided inter alia multisubstituted aromatic compounds useful for the inhibition of kallikrein, which compounds include substituted pyrazolyl or substituted triazolyl. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing certain diseases or disorders, which disease or disorder is amenable to treatment or prevention by the inhibition of kallikrein.

Abstract: A method for partitioning a molecular subset is described. The partitioning method takes into account molecular structure and its manner of storage and transmission, transformations to be applied to the molecular subset and their implementation, and constraints imposed by the implementation of the partitioning method. Using this method, a molecular subset can be stored, transmitted, and processed more efficiently. The resulting efficiency makes it possible to design and run applications which require complex molecular processing, such as rational drug discovery, virtual library design, etc.

Abstract: There are provided inter alia multisubstituted aromatic compounds useful for the inhibition of thrombin, which compounds include substituted pyrazolyl or substituted triazolyl. There are additionally provided pharmaceutical compositions. There are additionally provided methods of treating and preventing a disease or disorder, which disease or disorder is amenable to treatment or prevention by the inhibition of thrombin.

Abstract: Method and apparatus for the efficient computation of values for affinity functions for two or more molecular subsets of a molecular configuration, are provided. Either one or both of molecular subsets may be selected from a molecule library. Affinity engines can compute the affinity values, and can be synchronized in order to maximize utilization of processing power available in the affinity engines. A data path allocator can apportion molecular descriptor data to each affinity engine as one or more data blocks according to a data path schedule. Also, new configurations may be generated from one or more input configurations, computation of a plurality of affinity values for a plurality of configurations, and subsequent selection of processed configurations for further analysis.

Abstract: Computing units are determined for performing molecular docking calculations in parallel with the number of computing units and the width of the data paths allocated by relative complexity of operations. Data can be expected to arrive at downstream computing units as it is needed, leading to higher utilization of computing units. Computing units are hardware components that are specific to a calculation performed. For molecular docking calculations, functions of molecular subsets or of combinations of molecular subsets are calculated. Determinations include fit between molecular subsets, affinity or energy of “fit” between molecular subsets, etc. Affinity might include inter-atomic energy, bond energy, energy of atoms immersed in a field, etc. The calculations could be used to simulate and/or estimate likelihoods of molecular interactions.

Abstract: A method and apparatus for analysis of molecular combinations featuring two or more molecular subsets is described. The method computes the shape complementarity of the system utilizing a basis expansion representing molecular shapes of the first and second molecular subsets in a coordinate system. The precomputed sets of translated expansion coefficients for the first molecular subset are first constructed via application of a translation operator to a reference set of expansion coefficients and then stored on a computer recordable medium for later retrieval. Then, a shape complementarity score, representing a correlation of the first and second molecular subsets, is computed via suitable application of rotation operators to both the stored translated expansion coefficients of the first molecular subset and the reference expansion coefficients for the second molecular subset over the sequence of different sampled configurations for the molecular combination.

Abstract: A method for the prediction of adverse cross-reactions between lead candidate biomolecules and potential reactant molecules, often biopolymers, is described. In a computational system, reactions are modeled within a suitable environment, in order to determine a reaction profile between a lead candidate molecule and a potential reactant molecule. A risk assessment is then generated for each lead based on a plurality of reaction profiles for the lead with respect to a plurality of potential reactant molecules. The method includes provisions for redesign and optimization of the lead candidate, possibly iterative in nature, in order to avoid predicted adverse cross-reactions.

Abstract: A method and apparatus for estimating a location of one or more active sites on a target biopolymer molecular subset. The collective results for the likelihood of molecular combination between a collection of molecular subsets and the target biopolymer molecular subset are analyzed. The computational method utilizes an electrostatic affinity score for different configurations between the target biopolymer molecular subset and the molecular subsets of the collection. Favorable configurations are determined based on the affinity scores. These favorable configurations are then used to determine interaction loci, which are associated with regions of the target biopolymer molecular subset having a high likelihood of molecular combination. The locations of the active sites are then estimated from the interaction loci.

Abstract: A method and apparatus for analysis of molecular combinations featuring two or more molecular subsets is described. The computational method estimates the electrostatic affinity of the system via utilization of a basis expansion representing charge density and electrostatic potential functions associated with the first and second molecular subsets in a coordinate system. An electrostatic affinity, representing a correlation of the charge density and electrostatic potential functions of the first and second molecular subsets, is computed via suitable application of translation and rotation operators to the basis expansion coefficients over a sequence of different sampled configurations for the molecular combination. The method may also be combined with other methods for computation of shape complementarity in determining a composite or augmented score reflecting both electrostatic affinity and shape complementarity for configurations of a molecular combination.

Abstract: A method for partitioning a molecular subset is described. The partitioning method takes into account molecular structure and its manner of storage and transmission, transformations to be applied to the molecular subset and their implementation, and constraints imposed by the implementation of the partitioning method. Using this method, a molecular subset can be stored, transmitted, and processed more efficiently. The resulting efficiency makes it possible to design and run applications which require complex molecular processing, such as rational drug discovery, virtual library design, etc.