The Role of Conformational Dynamics in Abacavir-Induced Hypersensitivity Syndrome

[1]  A. Buckle,et al.  Integrating Experiment and Theory to Understand TCR-pMHC Dynamics , 2018, Front. Immunol..

[2]  James Fodor,et al.  Previously Hidden Dynamics at the TCR–Peptide–MHC Interface Revealed , 2018, The Journal of Immunology.

[3]  Andrew R. Jones,et al.  Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions , 2018, bioRxiv.

[4]  M. Delgado-Rodríguez,et al.  Systematic review and meta-analysis. , 2017, Medicina intensiva.

[5]  J. McCluskey,et al.  The role of HLA genes in pharmacogenomics: unravelling HLA associated adverse drug reactions , 2017, Immunogenetics.

[6]  S. Buus,et al.  Structural Elements Recognized by Abacavir-Induced T Cells , 2017, International journal of molecular sciences.

[7]  Lars V. Schäfer,et al.  Partial Dissociation of Truncated Peptides Influences the Structural Dynamics of the MHCI Binding Groove , 2017, Front. Immunol..

[8]  T. Takagi,et al.  Novel Concepts for Drug Hypersensitivity Based on the Use of Long-Time Scale Molecular Dynamic Simulation , 2016, Journal of pharmaceutics.

[9]  Gang Fu,et al.  PubChem Substance and Compound databases , 2015, Nucleic Acids Res..

[10]  C. Simmerling,et al.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. , 2015, Journal of chemical theory and computation.

[11]  Nathorn Chaiyakunapruk,et al.  Association of HLA-B*5701 genotypes and abacavir-induced hypersensitivity reaction: a systematic review and meta-analysis. , 2015, Journal of pharmacy & pharmaceutical sciences : a publication of the Canadian Society for Pharmaceutical Sciences, Societe canadienne des sciences pharmaceutiques.

[12]  A. Buckle,et al.  Understanding the structural dynamics of TCR-pMHC complex interactions. , 2014, Trends in immunology.

[13]  W. Pichler,et al.  Oxypurinol Directly and Immediately Activates the Drug-Specific T Cells via the Preferential Use of HLA-B*58:01 , 2014, The Journal of Immunology.

[14]  K. Garcia,et al.  TCR Scanning of Peptide/MHC through Complementary Matching of Receptor and Ligand Molecular Flexibility , 2014, The Journal of Immunology.

[15]  Pengfei Li,et al.  Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. , 2013, Journal of chemical theory and computation.

[16]  D. Margulies,et al.  Abacavir induces loading of novel self-peptides into HLA-B*57: 01 an autoimmune model for HLA-associated drug hypersensitivity , 2012, AIDS.

[17]  Jacqueline Adam,et al.  Avidity determines T‐cell reactivity in abacavir hypersensitivity , 2012, European journal of immunology.

[18]  J. McCluskey,et al.  Immune self-reactivity triggered by drug-modified HLA-peptide repertoire , 2012, Nature.

[19]  S. Mallal,et al.  Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire , 2012, Proceedings of the National Academy of Sciences.

[20]  Cyril F. Reboul,et al.  Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex , 2012, PLoS Comput. Biol..

[21]  Jan H. Jensen,et al.  Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. , 2011, Journal of chemical theory and computation.

[22]  Peter J. Stuckey,et al.  MUSTANG-MR Structural Sieving Server: Applications in Protein Structural Analysis and Crystallography , 2010, PloS one.

[23]  Lauren Wickstrom,et al.  Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. , 2009, Biophysical journal.

[24]  T. Cheatham,et al.  Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations , 2008, The journal of physical chemistry. B.

[25]  David Nolan,et al.  Human leukocyte antigen class I-restricted activation of CD8+ T cells provides the immunogenetic basis of a systemic drug hypersensitivity. , 2008, Immunity.

[26]  Mark M Davis,et al.  Spatial and temporal dynamics of T cell receptor signaling with a photoactivatable agonist. , 2007, Immunity.

[27]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[28]  S. Mallal,et al.  Prospective genetic screening decreases the incidence of abacavir hypersensitivity reactions in the Western Australian HIV cohort study. , 2006, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[29]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[30]  Natalie A Borg,et al.  T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I–bound peptide , 2005, Nature Immunology.

[31]  V. Nair,et al.  The antiviral activity, mechanism of action, clinical significance and resistance of abacavir in the treatment of pediatric AIDS. , 2005, Current pharmaceutical design.

[32]  A. Cutrell,et al.  Updated clinical risk factor analysis of suspected hypersensitivity reactions to abacavir , 2004, The Annals of pharmacotherapy.

[33]  N. Guler,et al.  Fluorouracil-induced neurotoxicity presenting with generalized tonic–clonic seizure , 2004, The Annals of pharmacotherapy.

[34]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[35]  Nathan A. Baker,et al.  PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations , 2004, Nucleic Acids Res..

[36]  Mark M Davis,et al.  Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation. , 2003, Molecular cell.

[37]  J. Walsh,et al.  The metabolic activation of abacavir by human liver cytosol and expressed human alcohol dehydrogenase isozymes. , 2002, Chemico-biological interactions.

[38]  Clive E. Bowman,et al.  Genetic variations in HLA-B region and hypersensitivity reactions to abacavir , 2002, The Lancet.

[39]  K. Anderson,et al.  Insights into the molecular mechanism of inhibition and drug resistance for HIV-1 RT with carbovir triphosphate. , 2002, Biochemistry.

[40]  O. Naderer,et al.  Hypersensitivity reactions during therapy with the nucleoside reverse transcriptase inhibitor abacavir. , 2001, Clinical therapeutics.

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

[42]  B. Brooks,et al.  Constant pressure molecular dynamics simulation: The Langevin piston method , 1995 .

[43]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[44]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[45]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[46]  D. Faulds,et al.  Abacavir , 2012, Drugs.

[47]  Berk Hess,et al.  P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation. , 2008, Journal of chemical theory and computation.