Synthetic Binding Proteins

A method for generating a binding protein that recognizes a rationally chosen recognition sequence, comprising:

• substituting a first amino acid with a second amino acid using site-directed mutagenesis of a member protein of a set of proteins at an identified position or positions correlated with recognition of a chosen specified target module.

A method for automating one or more steps in the flow diagram in FIG. 25A, comprising:

• utilizing a computer having programmed instructions to achieve one or more functions described in boxes 1, 2, 3, 4, 6, and 7B;
• and further utilizing an instrument capable of performing reactions to achieve any of steps 5, 7A or 8.

A method for automating one or more steps in the flow diagram in FIG. 25B using a computer for executing instructions and optionally automating one or more steps comprising chemical reactions.

An MmeI-like enzyme having a mutation resulting in at least one altered amino acid residue at a predetermined position that has a specificity for a DNA recognition sequence that is different by at least one base compared with the DNA recognition sequence of the unaltered enzyme.

A system comprising:

• a memory for storing instructions and a computer for executing the instructions, which when executed:
• create a set of binding proteins using an initial binding protein to query a database in a BLAST search, wherein each binding protein has a defined amino acid sequence, the amino acid sequences sharing an expectation value (E) of less than e-20 for sequences of more than 200 amino acids or less than e-10 for sequences of less than 200 amino acids;
• the binding proteins binding to specific target recognition sequences in a substrate, the target recognition sequences containing position-specific modules;

A system comprising:

• a memory for storing instructions and a computer for executing the instructions, which when executed:
• store positional information of an amino acid residue or amino acids residues in a first binding protein for targeted mutation to create a second binding protein having a predicted alteration of a module in a sequence position within a sequence of modules recognized by the protein.

A method or composition, comprising:

• any of the features disclosed in the attached description.