Abstract: The invention includes methods of representing polymer sequences in a way that reveals important position-specific contextual information. The representations can be used to determine a number of properties of polymers, such as protein and nucleic acid sequences, including the identification of secondary domain structures, folding rate constants, and the effects of altering (e.g., mutating) monomers. In addition, the representations can be used to compare polymers and thereby identify important structural and functional characteristics of polymers.

Abstract: The present invention provides methods and means for analyzing, designing, selecting and generating oligomer sequences, such as those for use in multiplex array-based nucleic acid probe systems, down to the selection of a single pair of optimal primer/target oligomers. Sequences are represented by a function of sequence context, called the context functional descriptor. In addition to the consideration of base pairing and nearest-neighbor analysis, the present computational methods incorporate the use of context functional descriptors and correlation matrices to account for higher-order thermodynamic interactions between nucleic acid sequences.

Abstract: The methods of the invention allow for the construction and/or use of modular computational models to accurately predict the therapeutic properties, including both therapeutic potency and one or more ADMET properties, of all or part of a chemical compound. The modular computational models can be used to rapidly screen libraries of chemical compounds, and reliably identify small subsets of those chemical compounds that have desirable therapeutic potency and ADMET properties, and are thus the best overall drug candidates.