Abstract: Provided herein are novel monoclonal antibodies and antibody fragments with improved binding to and/or neutralization against multiple SARS-CoV-2 variants, e.g., Omicron lineages. Also provided are compositions and biosensors comprising the monoclonal antibodies and antibody fragments and methods of using the novel monoclonal antibodies and antibody fragments for treating, preventing, and diagnosing COVID-19 and detecting SARS-CoV-2.

Abstract: Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a “structural footprint” to the cluster.

Abstract: Disclosed are computational methods, and associated hardware and software products for scoring conservation in a protein structure based on a computationally identified family or cluster of protein structures. A method of computationally identifying a family or cluster of protein structures in also disclosed herein.

Abstract: A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

Abstract: A set of known protein sequences associated with an organism is identified, wherein each known protein sequence comprises a plurality of ordered residues. A set of scores associated with a set of residues of the plurality of ordered residues is identified, wherein each score indicates a frequency of a residue in sequence context. A set of unique sub-sequences of the set of known protein sequences is identified. A plurality of protein signature residues is determined based on the set of scores associated with the set of residues and the set of unique sub-sequences.

Abstract: Disclosed are computational methods, and associated hardware and software products for scoring conservation in a protein structure based on a computationally identified family or cluster of protein structures. A method of computationally identifying a family or cluster of protein structures in also disclosed herein.

Abstract: Disclosed herein are computational methods of scoring or characterizing the specificity of residue to a protein of interest based on the frequency the residue occurs in local sequence context in a database. These scored residues can be used to identify protein signatures of interest that are useful, e.g., as targets in developing highly specific ligands for diagnostic or therapeutic uses.

Abstract: Disclosed are computational methods, and associated hardware and software products for scoring polypeptide residues that combine the use of a structure-based alignment with a method of selecting against confounding proteins. The scores can be used to identify protein signatures of interest that are useful, e.g., as targets in developing highly specific ligands for diagnostic or therapeutic uses.

Abstract: A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.