Proteins containing a C-terminal thioester are important intermediates in semi-synthesis. Currently there is one main method for the synthesis of protein thioesters that relies upon the use of engineered inteins. The invention involves, in some aspects a method, utilizing Sortase A, for preparation of recombinant proteins containing a C-terminal .sup.αthioester. This new method for double ligatation is useful for synthesizing new or naturally occurring molecules such as a protein thioester.

This invention relates to peptide microarrays, methods of generating peptide microarrays, and methods of identifying peptide binders using microarrays. More specifically, this invention relates to peptide microarrays, methods of generating peptide microarrays, and methods of identifying peptide binders using microarrays wherein the microarrays comprise cyclic peptides. The invention also relates to methods and compositions for detecting the formation of cyclized peptides from linear peptides on a microarray by contacting the microarray with a detectable protein. The cyclized peptides include tags that are activated upon cyclization, facilitating the detection of successful cyclization reactions. In additional aspects, the invention relates to developing fragmented peptide tags that, upon cyclization, bind to detectable proteins. Additionally, the invention relates to methods of generating linear and cyclic peptides subarrays on a microarray.

Methods for the preparation of sample polypeptide fractions are described. Sample polypeptides may be isolated from any of a variety of sources, including biological and non-biological systems. Sample polypeptides may be coupled or conjugated to other molecules to permit characterization of the sample polypeptide fractions. Sample polypeptide fractions may be prepared for analysis by a polypeptide assay.

The methods described herein provide a means of producing an array of spatially separated proteins. The method relies on covalently attaching each protein of the plurality of proteins to a structured nucleic acid particle (SNAP), and attaching the SNAPs to a solid support.

The invention relates to methods for preparing a compound comprising a peptide attached to a molecular scaffold whereby multiple peptide loops are formed, to compounds that can be obtained with such methods and uses thereof.

The methods described herein provide a means of producing an array of spatially separated proteins. The method relies on covalently attaching each protein of the plurality of proteins to a structured nucleic acid particle (SNAP), and attaching the SNAPs to a solid support.

A method and system is for searching a database to identify structures of molecular compounds from mass spectrometry data. Operations of the method and system include receiving a query for a target molecular structure in the database, the query representing a query spectrum; accessing a machine learning model trained with molecule-spectrum pairs; inputting the query spectrum into the machine learning model; generating, from the machine learning model, a score for each of one or more molecular structures, each score representing a probability that a molecular structure corresponds to the query spectrum; selecting, based on each of the scores, a small molecule; and outputting, on a user interface, a representation of the small molecule.

The present invention relates to artificial transcription factors (ATFs) that alter gene expression, including inducing pluripotency in cells or promoting the conversion of cells to specific cell fates. In particular, provided herein is a zinc-finger based ATF library that can be screened in cells by looking for expression of a specific gene (e.g., reporter expression), monitoring for cell surface markers or morphology, or via functional assays.

Peptides having activity as protein binding agents are disclosed. The peptides have the following structure (I): ##STR00001##
including stereoisomers, pharmaceutically acceptable salts and prodrugs thereof, wherein R, R.sup.1, L.sup.1, L.sup.2, G, M, Y.sup.1Y.sup.2 and SEQ are as defined herein. Methods associated with preparation and use of such peptides, as well as pharmaceutical compositions comprising such peptides, are also disclosed.

The invention relates to novel libraries of linear and cyclic peptides, and methods of generating and screening such libraries for biological, pharmaceutical and other uses.