Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances
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[1] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[2] Lars Malmström,et al. Cross-Link Guided Molecular Modeling with ROSETTA , 2013, PloS one.
[3] J. Adkins,et al. Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze , 2013, Journal of Structural and Functional Genomics.
[4] Juri Rappsilber,et al. Quantitative cross-linking/mass spectrometry using isotope-labelled cross-linkers☆ , 2013, Journal of proteomics.
[5] Li Yang,et al. In vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy. , 2013, Journal of proteome research.
[6] Meagan C. Burnet,et al. Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein–Protein Interactions by Chemical Cross-Linking , 2013, Journal of The American Society for Mass Spectrometry.
[7] Hong Liang,et al. A method for integrative structure determination of protein-protein complexes , 2012, Bioinform..
[8] R. Aebersold,et al. Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry , 2012, Science.
[9] J. E. Jimenez-Roldan,et al. Protein flexibility is key to cisplatin crosslinking in calmodulin , 2012, Protein science : a publication of the Protein Society.
[10] Friedrich Förster,et al. False discovery rate estimation for cross-linked peptides identified by mass spectrometry , 2012, Nature Methods.
[11] C. Lange,et al. Structural Insights into retinal guanylylcyclase-GCAP-2 interaction determined by cross-linking and mass spectrometry. , 2012, Biochemistry.
[12] Michael Götze,et al. Optimizing the enrichment of cross-linked products for mass spectrometric protein analysis. , 2012, Rapid communications in mass spectrometry : RCM.
[13] R. Aebersold,et al. Expanding the Chemical Cross-Linking Toolbox by the Use of Multiple Proteases and Enrichment by Size Exclusion Chromatography , 2012, Molecular & Cellular Proteomics.
[14] R. Aebersold,et al. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach , 2012, Proceedings of the National Academy of Sciences.
[15] Philip C. Andrews,et al. Quaternary Diamines as Mass Spectrometry Cleavable Crosslinkers for Protein Interactions , 2012, Journal of The American Society for Mass Spectrometry.
[16] Michael R Hoopmann,et al. Cross-linking Measurements of In Vivo Protein Complex Topologies* , 2011, Molecular & Cellular Proteomics.
[17] Lars Malmström,et al. Xwalk: computing and visualizing distances in cross-linking experiments , 2011, Bioinform..
[18] J. Rappsilber. The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes , 2011, Journal of structural biology.
[19] Valerie Daggett,et al. The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water , 2011, Protein science : a publication of the Protein Society.
[20] Valerie Daggett,et al. Generation of a consensus protein domain dictionary , 2011, Bioinform..
[21] David Baker,et al. Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System , 2010, mBio.
[22] D. Fabris,et al. Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D. , 2010, Journal of mass spectrometry : JMS.
[23] Fan Liu,et al. Combinatorial electrostatic collision-induced dissociative chemical cross-linking reagents for probing protein surface topology. , 2010, Analytical chemistry.
[24] Michael J MacCoss,et al. Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: a novel method to determine interresidue distances in protein structures through cross-linking. , 2010, Journal of proteome research.
[25] Michael A. Freitas,et al. Database search algorithm for identification of intact cross-links in proteins and peptides using tandem mass spectrometry. , 2010, Journal of proteome research.
[26] R. Aebersold,et al. Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics* , 2010, Molecular & Cellular Proteomics.
[27] R Dustin Schaeffer,et al. Dynameomics: a comprehensive database of protein dynamics. , 2010, Structure.
[28] P. Cramer,et al. Architecture of the RNA polymerase II–TFIIF complex revealed by cross-linking and mass spectrometry , 2010, EMBO Journal.
[29] R. Vachet,et al. Probing protein structure by amino acid-specific covalent labeling and mass spectrometry. , 2009, Mass spectrometry reviews.
[30] R. Zenobi,et al. Chemical cross-linking with NHS esters: a systematic study on amino acid reactivities. , 2009, Journal of mass spectrometry : JMS.
[31] A. Sinz,et al. Chances and pitfalls of chemical cross-linking with amine-reactive N-hydroxysuccinimide esters , 2008, Analytical and bioanalytical chemistry.
[32] Valerie Daggett,et al. Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations. , 2008, Protein engineering, design & selection : PEDS.
[33] R Dustin Schaeffer,et al. Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. , 2008, Protein engineering, design & selection : PEDS.
[34] Valerie Daggett,et al. Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data. , 2008, Protein engineering, design & selection : PEDS.
[35] Ruedi Aebersold,et al. Identification of cross-linked peptides from large sequence databases , 2008, Nature Methods.
[36] Malin M. Young,et al. Partial acetylation of lysine residues improves intraprotein cross-linking. , 2008, Analytical chemistry.
[37] D. Kern,et al. Dynamic personalities of proteins , 2007, Nature.
[38] Brett S Phinney,et al. Shotgun cross-linking analysis for studying quaternary and tertiary protein structures. , 2007, Journal of proteome research.
[39] Andrea Sinz,et al. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. , 2006, Mass spectrometry reviews.
[40] Malin M. Young,et al. Structure and dynamics of dark‐state bovine rhodopsin revealed by chemical cross‐linking and high‐resolution mass spectrometry , 2006, Protein science : a publication of the Protein Society.
[41] David A C Beck,et al. Methods for molecular dynamics simulations of protein folding/unfolding in solution. , 2004, Methods.
[42] K N Houk,et al. Quantitative evaluation of the lengths of homobifunctional protein cross‐linking reagents used as molecular rulers , 2001, Protein science : a publication of the Protein Society.
[43] Malin M. Young,et al. High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry , 2000, Proc. Natl. Acad. Sci. USA.
[44] Michael Levitt,et al. Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution , 1997 .
[45] M. Levitt,et al. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution , 1995 .