Artificial intelligence-based HDX (AI-HDX) prediction reveals fundamental characteristics to protein dynamics: Mechanisms on SARS-CoV-2 immune escape

[1]  O. S.,et al.  Accurate prediction of protein structures and interactions using a three-track neural network , 2022, Yearbook of Paediatric Endocrinology.

[2]  Cédric R. Weber,et al.  Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain , 2022, Cell.

[3]  R. Baric,et al.  Stopping pandemics before they start: Lessons learned from SARS-CoV-2 , 2022, Science.

[4]  N. Dean,et al.  The changing epidemiology of SARS-CoV-2 , 2022, Science.

[5]  A. Walls,et al.  Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement , 2021, bioRxiv.

[6]  J. Muñóz-Valle,et al.  Overview of Neutralizing Antibodies and Their Potential in COVID-19 , 2021, Vaccines.

[7]  S. Karamanou,et al.  Probing Universal Protein Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy. , 2021, Analytical chemistry.

[8]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[9]  S. Marqusee,et al.  The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes , 2021, Nature Structural & Molecular Biology.

[10]  S. Dübel,et al.  A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients binds to the ACE2-RBD interface and is tolerant to most known RBD mutations , 2021, Cell Reports.

[11]  S. Lindert,et al.  Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data. , 2021, Journal of chemical theory and computation.

[12]  A. Borysik,et al.  HDXmodeller: an online webserver for high-resolution HDX-MS with auto-validation , 2021, Communications Biology.

[13]  Yasushi Okuno,et al.  Extraction of protein dynamics information from cryo-EM maps using deep learning , 2021, Nature Machine Intelligence.

[14]  Derek J. Wilson,et al.  Protein Footprinting, Conformational Dynamics, and Core Interface-Adjacent Neutralization “Hotspots” in the SARS-CoV-2 Spike Protein Receptor Binding Domain/Human ACE2 Interaction , 2020, Journal of the American Society for Mass Spectrometry.

[15]  G. Lin,et al.  TMPSS: A Deep Learning-Based Predictor for Secondary Structure and Topology Structure Prediction of Alpha-Helical Transmembrane Proteins , 2021, Frontiers in Bioengineering and Biotechnology.

[16]  Olivér Ozohanics,et al.  Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes , 2020, Life.

[17]  B. Ramaswamy,et al.  Estrogen Receptor Beta (ERβ): A Ligand Activated Tumor Suppressor , 2020, Frontiers in Oncology.

[18]  P. MacAry,et al.  SARS-CoV-2 S protein ACE2 interaction reveals novel allosteric targets , 2020, bioRxiv.

[19]  R. Welsh,et al.  Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail , 2020, Science.

[20]  Amalio Telenti,et al.  Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody , 2020, Nature.

[21]  Lei Guo,et al.  Accurate classification of membrane protein types based on sequence and evolutionary information using deep learning , 2019, BMC Bioinformatics.

[22]  P. Griffin,et al.  Protein dynamics and conformational changes explored by hydrogen/deuterium exchange mass spectrometry. , 2019, Current opinion in structural biology.

[23]  Jie Zheng,et al.  Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments , 2019, Nature Methods.

[24]  M. J. Chalmers,et al.  Interlaboratory Comparison of Hydrogen-Deuterium Exchange Mass Spectrometry Measurements of the Fab Fragment of NISTmAb. , 2019, Analytical chemistry.

[25]  Martin Eisenacher,et al.  The PRIDE database and related tools and resources in 2019: improving support for quantification data , 2018, Nucleic Acids Res..

[26]  Rémy Sounier,et al.  Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex , 2018, bioRxiv.

[27]  Yu-Yen Ou,et al.  DeepEfflux: a 2D convolutional neural network model for identifying families of efflux proteins in transporters , 2018, Bioinform..

[28]  Jian Wang,et al.  Assembling the Community-Scale Discoverable Human Proteome , 2018, Cell systems.

[29]  Daniel Henrion,et al.  Membrane and Nuclear Estrogen Receptor Alpha Actions: From Tissue Specificity to Medical Implications. , 2017, Physiological reviews.

[30]  John R Engen,et al.  Conformational insight into multi-protein signaling assemblies by hydrogen-deuterium exchange mass spectrometry. , 2016, Current opinion in structural biology.

[31]  Joshua S. Yuan,et al.  Phytoestrogens and Mycoestrogens Induce Signature Structure Dynamics Changes on Estrogen Receptor α , 2016, International journal of environmental research and public health.

[32]  Peter B. McGarvey,et al.  UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches , 2014, Bioinform..

[33]  B. Schuler,et al.  Single-molecule spectroscopy of protein folding dynamics--expanding scope and timescales. , 2013, Current opinion in structural biology.

[34]  G. Vriend,et al.  Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function , 2012, PloS one.

[35]  T. Foster Role of estrogen receptor alpha and beta expression and signaling on cognitive function during aging , 2012, Hippocampus.

[36]  A. Biegert,et al.  HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.

[37]  Asifullah Khan,et al.  Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition. , 2011, Journal of theoretical biology.

[38]  Xin Zhou,et al.  HDX-Analyzer: a novel package for statistical analysis of protein structure dynamics , 2011, BMC Bioinformatics.

[39]  Lantao Liu,et al.  Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum , 2010, BMC Bioinformatics.

[40]  F. S. Mathews,et al.  A joint x-ray and neutron study on amicyanin reveals the role of protein dynamics in electron transfer , 2010, Proceedings of the National Academy of Sciences.

[41]  Yong Wang,et al.  Unique ligand binding patterns between estrogen receptor alpha and beta revealed by hydrogen-deuterium exchange. , 2009, Biochemistry.

[42]  Ding Xuemei,et al.  Thermostable carbohydrate binding module increases the thermostability and substrate-binding capacity of Trichoderma reesei xylanase 2. , 2009, New biotechnology.

[43]  R. Dror,et al.  Long-timescale molecular dynamics simulations of protein structure and function. , 2009, Current opinion in structural biology.

[44]  Yong Wang,et al.  Prediction of the tissue-specificity of selective estrogen receptor modulators by using a single biochemical method , 2008, Proceedings of the National Academy of Sciences.

[45]  K. Dahlman-Wright,et al.  Review Nuclear Receptor Signaling | The Open Access Journal of the Nuclear Receptor Signaling Atlas Estrogen receptor β: an overview and update , 2022 .

[46]  M. Karplus,et al.  A hierarchy of timescales in protein dynamics is linked to enzyme catalysis , 2007, Nature.

[47]  Margaret Warner,et al.  Estrogen receptors: how do they signal and what are their targets. , 2007, Physiological reviews.

[48]  W. Atchley,et al.  Solving the protein sequence metric problem. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[49]  A. Liwo,et al.  Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[50]  H. Balakrishnan,et al.  Compatibility of alkaline xylanases from an alkaliphilic Bacillus NCL (87-6-10) with commercial detergents and proteases , 2004, Journal of Industrial Microbiology and Biotechnology.

[51]  Virgil L. Woods,et al.  Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[52]  P. Christakopoulos,et al.  Antimicrobial activity of acidic xylo-oligosaccharides produced by family 10 and 11 endoxylanases. , 2003, International journal of biological macromolecules.

[53]  Amos Bairoch,et al.  Detailed peptide characterization using PEPTIDEMASS – a World‐Wide‐Web‐accessible tool , 1997, Electrophoresis.

[54]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[55]  B. Rost,et al.  Conservation and prediction of solvent accessibility in protein families , 1994, Proteins.

[56]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.