Patent Document ID: 8036867
Application ID: 10967085
Patent Flag: 1

Claim One:
1. A method for determining whether a biomolecule is a lead candidate by using a computational system to compute an affinity function between two or more molecular subsets of a molecular configuration of the biomolecule or target or both defined by a configuration dataset, the method comprising: assigning to each of the molecular subsets one or more molecular descriptors associated with the molecular configuration of the biomolecule or target or both, wherein each molecular descriptor represents one or more properties or elements of a molecular subset; storing, in a descriptor data storage, the assigned molecular descriptors as molecular descriptor data; allocating, with a data path allocator that is a circuit of the computational system, the molecular descriptor data to a plurality of data paths associated with a plurality of affinity engines, each being a separate circuit of the computational system; for each data path: partitioning the molecular descriptor data allocated to the respective data path into a plurality of data blocks; and routing the data blocks to the respective data path according to a data path schedule that specifies a rate that the data blocks are sent in sequence along the respective data path and specifies a size of a respective data block, wherein the data path schedule takes into account the amount of processing needed for calculating an affinity component for all or part of the molecular descriptor data and the amount of processing power available from each affinity engine so as to reduce a synchronization lag between affinity engines; transmitting the molecular descriptor data from the descriptor data storage to the plurality of affinity engines, wherein transmitting uses the plurality of data paths; generating, with the plurality of affinity engines, affinity component results for the molecular configuration, wherein each affinity engine includes one or more processing pipelines, wherein each affinity engine generates results for only one affinity component, wherein each affinity component corresponds to a different type of interaction energy between the molecular subsets; accumulating affinity function values based on affinity component results generated by the plurality of affinity engines and received by an affinity component accumulator; and determining whether a biomolecule is a lead candidate based on the accumulated affinity function values.