AIMC Topic: Protein Stability

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Unified rational protein engineering with sequence-based deep representation learning.

Nature methods Oct 21, 2019
Rational protein engineering requires a holistic understanding of protein function. Here, we apply deep learning to unlabeled amino-acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically...
Mutation Amino Acid Sequence Protein Stability Protein Engineering Deep Learning
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Seq2seq Fingerprint with Byte-Pair Encoding for Predicting Changes in Protein Stability upon Single Point Mutation.

IEEE/ACM transactions on computational biology and bioinformatics Apr 1, 2019
The engineering of stable proteins is crucial for various industrial purposes. Several machine learning methods have been developed to predict changes in the stability of proteins corresponding to single point mutations. To improve the prediction acc...
Databases, Genetic Proteins Unsupervised Machine Learning Amino Acid Sequence Humans Neural Networks, Computer Computational Biology Protein Stability Sequence Analysis, Protein Point Mutation
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DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks.

Journal of chemical information and modeling Feb 25, 2019
Accurately predicting changes in protein stability due to mutations is important for protein engineering and for understanding the functional consequences of missense mutations in proteins. We have developed DeepDDG, a neural network-based method, fo...
Neural Networks, Computer Computational Biology Proteins Protein Stability Transition Temperature Point Mutation
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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife Jun 21, 2018
Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational ap...
Protein Binding Models, Molecular Gene Expression Kinetics Humans Machine Learning Animals Crystallography, X-Ray Binding Sites Protein Engineering Thermodynamics Amino Acid Sequence Protein Stability Receptor, Serotonin, 5-HT2C Serotonin 5-HT2 Receptor Antagonists Protein Conformation, alpha-Helical Sequence Alignment Protein Conformation, beta-Strand Sequence Homology, Amino Acid Point Mutation Protein Interaction Domains and Motifs Serotonin 5-HT2 Receptor Agonists
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PON-tstab: Protein Variant Stability Predictor. Importance of Training Data Quality.

International journal of molecular sciences Mar 28, 2018
Several methods have been developed to predict effects of amino acid substitutions on protein stability. Benchmark datasets are essential for method training and testing and have numerous requirements including that the data is representative for the...
Machine Learning Proteins Databases, Protein Models, Molecular Protein Stability
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Predicting the Effect of Single and Multiple Mutations on Protein Structural Stability.

Molecules (Basel, Switzerland) Jan 27, 2018
Predicting how a point mutation alters a protein's stability can guide pharmaceutical drug design initiatives which aim to counter the effects of serious diseases. Conducting mutagenesis studies in physical proteins can give insights about the effect...
Amino Acid Substitution Thermodynamics Proteins Mutation Protein Stability Protein Conformation Computer Simulation Support Vector Machine Decision Trees Neural Networks, Computer
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Stability of infliximab solutions in different temperature and dilution conditions.

Journal of pharmaceutical and biomedical analysis Dec 18, 2017
Infliximab is a monoclonal antibody widely used for the treatment of inflammatory diseases. Over the past few years, many studies have assessed that monoclonal antibodies are prone to aggregation under stress conditions. The aim of this study was to ...
Nephelometry and Turbidimetry Peptide Mapping Spectrophotometry, Ultraviolet Chromatography, Gel Chromatography, Ion Exchange Spectroscopy, Fourier Transform Infrared Pharmaceutical Solutions Drug Stability Temperature Infliximab Technology, Pharmaceutical Drug Compounding Biosimilar Pharmaceuticals Time Factors Antirheumatic Agents Osmolar Concentration Protein Stability Nanoparticles Protein Aggregates
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and cell-based analyses reveal strong divergence between prediction and observation of T-cell-recognized tumor antigen T-cell epitopes.

The Journal of biological chemistry May 23, 2017
Tumor exomes provide comprehensive information on mutated, overexpressed genes and aberrant splicing, which can be exploited for personalized cancer immunotherapy. Of particular interest are mutated tumor antigen T-cell epitopes, because neoepitope-s...
Melanoma Reproducibility of Results Animals Computational Biology Cancer Vaccines Antigens, Neoplasm Vaccines, Synthetic Expert Systems Humans Oligopeptides Artificial Intelligence Immunogenicity, Vaccine Cells, Cultured Mice, Transgenic Peptide Fragments Epitopes Models, Immunological Membrane Proteins HLA-A2 Antigen Protein Refolding Neoplasm Proteins Protein Stability T-Lymphocytes, Cytotoxic Mice, Knockout
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Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity.

Journal of immunology (Baltimore, Md. : 1950) Jul 8, 2016
Binding of peptides to MHC class I (MHC-I) molecules is the most selective event in the processing and presentation of Ags to CTL, and insights into the mechanisms that govern peptide-MHC-I binding should facilitate our understanding of CTL biology. ...
Antigen Presentation Lymphocyte Activation Histocompatibility Antigens Class I Protein Stability Humans Neural Networks, Computer Epitopes, T-Lymphocyte Peptides
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Biosimilarity Assessments of Model IgG1-Fc Glycoforms Using a Machine Learning Approach.

Journal of pharmaceutical sciences Dec 30, 2015
Biosimilarity assessments are performed to decide whether 2 preparations of complex biomolecules can be considered "highly similar." In this work, a machine learning approach is demonstrated as a mathematical tool for such assessments using a variety...
Machine Learning Immunoglobulin G Biosimilar Pharmaceuticals Protein Stability Immunoglobulin Fc Fragments
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