Abstract: Disclosed herein are methods for predicting immunogenicity of a candidate peptide. The method comprises obtaining a three-dimensional candidate structural representation of the candidate peptide bound to an antigen presenting molecule; obtaining a plurality of candidate measurements; and predicting, with an electronic processor, the immunogenicity of the candidate peptide based upon the plurality of candidate measurements. Further disclosed herein are methods for producing vaccines. The method for producing a vaccine comprises predicting immunogenicity of one or more candidate peptides using the methods described herein, and producing a vaccine comprising one or more peptides predicted to be immunogenic.

Abstract: Described are methods for predicting affinity of a candidate molecule for a second molecule. The method comprises obtaining a three-dimensional candidate structural representation of the candidate molecule bound to a second molecule; obtaining a plurality of candidate measurements, wherein each candidate measurement is associated with at least one feature of the candidate structural representation; and predicting, with an electronic processor, the affinity of the candidate molecule for the second molecule, wherein the electronic processor is configured to predict the affinity of the candidate molecule for the second molecule based upon the plurality of candidate measurements. The candidate molecule may be a peptide, such as a neoantigen, a viral peptide, a non-mutated self peptide, or a post-translationally modified peptide. The second molecule may be an antigen presenting molecule, such as a class I MHC molecule or a class II MHC molecule.

Abstract: Disclosed are computational modeling methods employing RMS fluctuation values associated with energy functions to compute binding properties of a subject biomolecule and an identified target. An energy function (or force field) that relates the molecular structure of a biomolecule to an energy value, modified with terms calculated from sets of RMS fluctuation values of the biomolecule, the target and the complex, are used to identify a potential mutation or modification suitable for imparting a selected property to a biomolecule of interest. Uses of the method in the manufacture of non-native proteins having a selected modified property are also provided. Therapeutic agents (proteins, antibodies, TCRs) enzymes, etc., prepared according to the present methods are also provided. Non-native biomolecules having improved properties, for example, weaker or enhanced binding affinity in a modified TCR, are described. Enzymes, industrial reagents, and the like, created using the disclosed methods are also presented.

Abstract: The present disclosure relates, in part, to MS apparatus, methods, and/or software, having improved selectivity, sensitivity, specificity, resolution, mass accuracy and dynamic range over conventional MS technologies. In particular, the technology relates to apparatus, methods, and/or software wherein a combination of in-source fragmentation, ion mobility separation, and/or time-aligned parallel (TAP) sample ion fragmentations are utilized in mass spectrometry for the analysis of samples.

Abstract: The present disclosure relates, in part, to MS apparatus, methods, and/or software, having improved selectivity, sensitivity, specificity, resolution, mass accuracy and dynamic range over conventional MS technologies. In particular, the technology relates to apparatus, methods, and/or software wherein a combination of in-source fragmentation, ion mobility separation, and/or time-aligned parallel (TAP) sample ion fragmentations are utilized in mass spectrometry for the analysis of samples.

Abstract: The present invention relates to phosphonate, nucleoside phosphonate or nucleoside phosphate compounds, compositions containing them, processes for obtaining them, and their use in treating a variety of medical disorders, in particular viral infections, cancers and the like.

Abstract: The present invention relates to phosphonate, nucleoside phosphonate or nucleoside phosphate compounds, compositions containing them, processes for obtaining them, and their use in treating a variety of medical disorders, in particular viral infections, cancers and the like.