The present invention revealed that translating an mRNA that encodes a peptide containing an unnatural amino acid in a translation system that contains a ribosome containing an engineered L31 protein can increase the amount of the translated peptide. Furthermore, the invention revealed that by using this ribosome, the relative amount of by-products can also be reduced. An engineered L31 protein of the present invention has an amino acid sequence with deletion of 6 or more amino acid residues from the C terminus in the amino acid sequence of the wild-type Escherichia coli L31 protein.

The invention provides compositions and methods for binding Ras in a nucleotide free state (apo RAS) and inhibiting Ras signaling. In one embodiment, the invention provides monobodies that specifically bind apo RAS and methods of use. Thus, in diseases and conditions where a reduction of Ras signaling is beneficial, such inhibitory compositions act as therapeutics.

Provided are methods and compositions for the production of novel antibodies that bind specifically to a target antigen. These methods and compositions are particularly useful for producing antibodies having the antigen binding specificity of a reference antibody but with improved properties (e.g., binding affinity, immunogenicity, and thermodynamic stability) relative to the reference antibody.

Provided are methods and compositions for the production of novel antibodies that bind specifically to a target antigen. These methods and compositions are particularly useful for producing antibodies having the antigen binding specificity of a reference antibody but with improved properties (e.g., binding affinity, immunogenicity, and thermodynamic stability) relative to the reference antibody.

The invention relates to a method for selecting a sequence set from a library of expressed nucleic acid sequences, wherein cells are provided, each cell comprises an expressed nucleic acid sequence expressed as a target protein. The cells are encapsulated by treating them with a cationic polysaccharide and subsequently treating them with an anionic polysaccharide, yielding encapsulated cells, perforating the membrane of the encapsulated cells, yielding solubilized compartments, contacting them with a ligand to said target protein, the ligand bearing a detectable label, and selecting a subset of solubilized compartments as a function of detectable label and isolating the expressed nucleic acid sequences from the selection as a selected sequence set.

The invention relates to a method for selecting a sequence set from a library of expressed nucleic acid sequences, wherein cells are provided, each cell comprises an expressed nucleic acid sequence expressed as a target protein. The cells are encapsulated by treating them with a cationic polysaccharide and subsequently treating them with an anionic polysaccharide, yielding encapsulated cells, perforating the membrane of the encapsulated cells, yielding solubilized compartments, contacting them with a ligand to said target protein, the ligand bearing a detectable label, and selecting a subset of solubilized compartments as a function of detectable label and isolating the expressed nucleic acid sequences from the selection as a selected sequence set.

Provided are methods for efficiently and comprehensively screening antibody repertoires from B cells to obtain and produce molecules with binding characteristics and functional activities for use in human therapy.

A method of identifying an extant protein, including (a) providing inputs including: (i) a binding profile, wherein the binding profile includes a plurality of binding outcomes for binding of the extant protein to a plurality of different affinity reagents, wherein individual binding outcomes of the plurality of binding outcomes include a measure of binding between the extant protein and a different affinity reagent of the plurality of different affinity reagents, (ii) a database including information characterizing or identifying a plurality of candidate proteins, and (iii) a binding model; (b) determining a probability for each of the affinity reagents binding to each of the candidate proteins in the database according to the binding model; and (c) identifying the extant protein as a selected candidate protein having a probability for binding each of the affinity reagents that is most compatible with the binding profile for the extant protein.

A method of identifying an extant protein, including (a) providing inputs including: (i) a binding profile, wherein the binding profile includes a plurality of binding outcomes for binding of the extant protein to a plurality of different affinity reagents, wherein individual binding outcomes of the plurality of binding outcomes include a measure of binding between the extant protein and a different affinity reagent of the plurality of different affinity reagents, (ii) a database including information characterizing or identifying a plurality of candidate proteins, and (iii) a binding model; (b) determining a probability for each of the affinity reagents binding to each of the candidate proteins in the database according to the binding model; and (c) identifying the extant protein as a selected candidate protein having a probability for binding each of the affinity reagents that is most compatible with the binding profile for the extant protein.

Some aspects of this disclosure relate to systems, apparatuses, compositions (e.g., isolated nucleic acids and vectors), and methods for improving the stability and/or solubility of proteins evolved using phage-assisted continuous evolution (PACE). In some embodiments, vectors described herein comprise nucleic acids encoding selection systems (e.g., positive and/or negative selection systems) that link expression of genes required for production of infectious phage particles to a desirable physiochemical (e.g., stability or solubility) and/or desired function of an evolved protein.