Abstract: The invention relates to system and method for generating an antibody library. Specifically, the invention relates to a computer-implemented system and method for generating a library of antibodies based on a predetermined epitope.

Abstract: This disclosure presents methods for antibody structure prediction and design. We utilize the growing number of antibody structures and sequences are used with powerful protein modeling methods to design and predict antibody structural models up to sub-angstrom accuracy. The invention also relates to systems and methods for generating an antibody library. Specifically, the invention relates to computer-implemented systems and methods for generating an antibody library for a predetermined epitope. The invention further relates to determining structural models of the interface between an antibody and its antigen. The invention also relates to determining structural models of an unbound complementarity determining region of an antibody.

Abstract: The present invention provides enzymes that have been optimized by implementation of Protein Repair One Stop Shop (PROSS), an algorithm that generates protein design(s) for enhanced stability without changing either enzymatic properties or enzyme active site conformation of the respective enzyme. The protein design(s) generated by PROSS introduce mutations to the amino acid sequence of a wild-type protein, resulting in a mutated amino acid sequence that encodes a variant of the wild-type enzyme, i.e., “an enzyme variant”, which has an enhanced stability, core packing, surface polarity and backbone rigidity, a higher functional expression, and/or a combination thereof, compared to the stability core packing, surface polarity and backbone rigidity, functional expression and/or a combination thereof, of the wild-type enzyme.

Abstract: The present invention provides enzymes that have been optimized by implementation of Protein Repair One Stop Shop (PROSS), an algorithm that generates protein design(s) for enhanced stability without changing either enzymatic properties or enzyme active site conformation of the respective enzyme. The protein design(s) generated by PROSS introduce mutations to the amino acid sequence of a wild-type protein, resulting in a mutated amino acid sequence that encodes a variant of the wild-type enzyme, i.e., an enzyme variant, which has an enhanced stability, core packing, surface polarity and backbone rigidity, a higher functional expression, and/or a combination thereof, compared to the stability core packing, surface polarity and backbone rigidity, functional expression and/or a combination thereof, of the wild-type enzyme.

Abstract: This disclosure relates to antibodies and antigen-binding fragments that bind specifically to Vascular endothelial growth factor (VEGF), and prophylactic, diagnostic, and therapeutic methods of using the same.

Abstract: Methods for computational affinity maturation are described wherein a candidate antibody sequence is optimized for affinity, stability, or both, first utilizing computational saturation mutagenesis to identify and mutations at those positions that satisfy a predefined first threshold of affinity score or stability score, generating sequences comprising all combinations of the mutations at each position, computing the affinity score, stability score, or both and ranking the variant antibody sequences according to a predefined second threshold, then from the affinity score or stability score of all generated sequences identify the optimized antibody sequences. The method is ideally carried out on multiple CPUs where a server generates the sequences, the CPUs evaluate the affinity or stability score, reports the results to the server, which ranks all of the data from the CPUs to identify the optimal candidates.

Abstract: This disclosure relates to antibodies and antigen-binding fragments that bind specifically to Programmed cell death protein 1 (PD-1), and prophylactic, diagnostic, and therapeutic methods of using the same.

Abstract: The invention relates to system and method for generating an antibody library. Specifically, the invention relates to a computer-implemented system and method for generating a library of antibodies based on a predetermined epitope.

Abstract: The invention relates to systems and methods for generating a polypeptide library. Specifically, the invention relates to computer-implemented systems and methods for generating a library of polypeptides, for example, antibodies.