Just-evotec Biologics, Inc.

Jeremy Martin Shaver

Randal Robert Ketchem

Tileli Amimeur

Joshua R Smith

Rutilio Clark

Alison J Gillespie

Fernando Garcia

Michael W Vandiver

Brian W Horman

Fernando Garcia Morales

John Alex Taylor

Ron Gillespie

The concepts described herein are directed to implementations of production facilities that can produce molecules used to treat biological conditions, such as biotherapeutics. The biotherapeutics can include various molecules, such as proteins, enzymes, and antibodies. The production facilities can include a number of separate modular cleanrooms that comprise particular pieces of equipment to perform one or more aspects of the processes used to manufacture biotherapeutics. The modular cleanrooms are arranged such that material that is produced by the equipment of one modular cleanroom can be transferred to another modular cleanroom for additional processing. Additionally, systems and processes are described to generate models using machine learning techniques, where the models can be used to predict productivity and/or efficiency metrics for production lines of biotherapeutics. Further, models can be generated to control the operation of pieces of equipment included in the production lines.

Facilities and processes to produce biotherapeutics

Amino acid sequences of proteins can be produced using one or more generative machine learning architectures. The amino acid sequences produced by the one or more generative machine learning architectures can be used to train a classification model architecture. The classification model architecture can classify amino acid sequences according to a number of classifications. Individual classifications of the number of classifications can correspond to at least one of a structural feature of proteins, a range of values of a structural feature of proteins, a biophysical property of proteins, or a range of values of a biophysical property of proteins.

Implementing a generative machine learning architecture to produce training data for a classification model

Amino acid sequences of proteins can be produced using an autoencoder. For example, amino acid sequences of variant proteins can be produced by an autoencoder that is fed an amino acid sequence of a base protein as input. A decoding component of the autoencoder can include at least one or more components of a generative adversarial network.

Autoencoder with generative adversarial network to generate protein sequences

A system for generating a model for predicting a molecular property of a variant of a molecule is provided. For each of a plurality of variants of the molecule, the system for each structural feature, aggregates the values for the structural features of the residues of the molecule that were modified to form the variant to form a feature vector for the variant. The system assigns the value for the molecular property of the variant to the feature vector wherein the feature vector and the assigned value form training data. The system then generates the model for predicting a value for the molecular property using the training data for the plurality of variants.

Predicting molecular properties of molecular variants using residue-specific molecular structural features

Amino acid sequences of antibodies can be generated using a generative adversarial network that includes a first generating component that generates amino acid sequences of antibody light chains and a second generating component generates amino acid sequences of antibody heavy chains. Amino acid sequences of antibodies can be produced by combining the respective amino acid sequences produced by the first generating component and the second generating component. The training of the first generating component and the second generating component can proceed at different rates. Additionally, the antibody amino acids produced by combining amino acid sequences from the first generating component and the second generating component may be evaluated according to complentarity-determining regions of the antibody amino acid sequences. Training datasets may be produced using amino acid sequences that correspond to antibodies have particular binding affinities with respect to molecules, such as binding affinity with major histocompatibility complex (MHC) molecules.

Generation of protein sequences using machine learning techniques

Disclosed are methods for interrogating the physiochemical properties of a protein of interest, including method for predicting the stability of a protein at low pH, such as may be encountered during a manufacturing viral inactivation step.

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Lake Forest Park, WA, United States of America

Jeremy Martin Shaver