Abstract: Mechanisms for molecule design using machine learning include: forming a first training set for a neural network using, for each of a first plurality of known molecules, a plurality of input values that represent the structure of the known molecule and a plurality of functional property values for the known molecule; training the neural network using the first training set; proposing a first plurality of proposed molecules, and predicting first predicted functional property values of the first plurality of proposed molecules that have the desired function property values; causing the first plurality of proposed molecules to be synthesized to form a first plurality of synthesized molecules; receiving first measured functional property values of the first plurality of synthesized molecules; and adding data regarding the first plurality of synthesized molecules to the first training set to form a second training set and retrain the neural network using the second training set.

Abstract: Methods and systems for predicting functions of molecular sequences, comprising: generating an array that represents a sequence of molecules; determining a projection of the sequence of molecules, wherein the determining comprises multiplying a representation of the array that represents the sequence of the molecules by a first hidden layer matrix that represents a number of possible sequence dependent functions, wherein the first hidden layer matrix is determined during training of a neural network; and determining a function of the sequence of molecules by applying a plurality of weights to a representation of the projection of the sequence of molecules, wherein the plurality of weights is determined during the training of the neural network.

Abstract: The present invention provides method of identifying molecules that cooperatively and positively interact with either a ligand or a target molecule of a ligand/target molecule pair, or molecules that interact with a ligand/target molecule complex.

Abstract: The present invention provides improved methods for generating fluorescent aptamer polynucleotides, novel polynucleotides, and methods for use thereof.

Abstract: A microarray has a substrate and a plurality of three-dimensional microstructures formed on the substrate. Each of the three-dimensional microstructures is made with polymer material and has a plurality of reactive sites formed on its surface and interior pores. The polymer material is polymer gel or other porous polymer. The combination of three-dimensional microstructure and porous polymer material increases the surface area of the microstructure and density of the reactive sites on the surface of the microstructures. The higher density of reactive sites increases the luminescence, visibility or instrument detectability of the interaction between analytes and reactive microstructure sites on the microarray. A plurality of chemical groups are respectively attached to the reactive sites. The chemical groups each include at least one monomer. The chemical groups may have different chemical structures. A plurality of microchannels can be formed around the microstructures for isolation.

Abstract: A method of identifying the presence or absence of a DNA molecule in a test sample comprising a specific DNA sequence is disclosed. In one embodiment, the method comprises the steps of mixing a test sample with a peptide/dye conjugate comprising a covalently linked peptide and a dye, wherein the peptide binds to the specific DNA sequence and wherein the peptide/dye conjugate will fluoresce if the peptide is bound to the specific DNA sequence, and measuring fluorescence, wherein specific fluorescence above background level indicates that the conjugate is bound to the specific DNA sequence. In another embodiment, the present invention is a method of cleaving a specific DNA molecule and a test sample. The method comprises mixing a test sample with a peptide dye conjugate comprising a covalently linked peptide and a dye, wherein the peptide binds to the specific DNA sequence and wherein the peptide dye conjugate will cleave if the peptide is bound to a specific DNA sequence.