Computational tools and resources for pseudokinase research
Tài liệu tham khảo
Aquino, 2018
Baker, 2001, Electrostatics of nanosystems: Application to microtubules and the ribosome, Proceedings of the National Academy of Sciences of the United States of America, 98, 10037, 10.1073/pnas.181342398
Berginski, 2020, The dark kinase knowledgebase: An online compendium of knowledge and experimental results of understudied kinases, Nucleic Acids Research, 49, D529, 10.1093/nar/gkaa853
Capra, 2007, Predicting functionally important residues from sequence conservation, Bioinformatics, 23, 1875, 10.1093/bioinformatics/btm270
Chatzou, 2016, Multiple sequence alignment modeling: Methods and applications, Briefings in Bioinformatics, 17, 1009, 10.1093/bib/bbv099
Crooks, 2004, WebLogo: A sequence logo generator, Genome Research, 14, 1188, 10.1101/gr.849004
Eyers, 2015, Tribbles: A twist in the pseudokinase tail, Structure, 23, 1974, 10.1016/j.str.2015.10.003
Eyers, 2020, Marveling at the incredible ULK4, Structure, 28, 1181, 10.1016/j.str.2020.10.005
Eyers, 2017, Tribbles in the 21st century: The evolving roles of tribbles pseudokinases in biology and disease, Trends in Cell Biology, 27, 284, 10.1016/j.tcb.2016.11.002
Eyers, 2013, Dawn of the dead: Protein pseudokinases signal new adventures in cell biology, Biochemical Society Transactions, 41, 969, 10.1042/BST20130115
Foulkes, 2018, Covalent inhibitors of EGFR family protein kinases induce degradation of human tribbles 2 (TRIB2) pseudokinase in cancer cells, Science Signaling, 11, eaat7951, 10.1126/scisignal.aat7951
Gosal, 2011, ProKinO: An ontology for integrative analysis of protein kinases in cancer, PLoS One, 6, 10.1371/journal.pone.0028782
Grütter, 2013, Structural characterization of the RLCK family member BSK8: A pseudokinase with an unprecedented architecture, Journal of Molecular Biology, 425, 4455, 10.1016/j.jmb.2013.07.034
Hanks, 1995, The eukaryotic protein kinase superfamily: Kinase (catalytic) domain structure and classification1, The FASEB Journal, 9, 576, 10.1096/fasebj.9.8.7768349
Haydon, 2003, Identification of novel phosphorylation sites on Xenopus laevis Aurora A and analysis of phosphopeptide enrichment by immobilized metal-affinity chromatography, Molecular & Cellular Proteomics: MCP, 2, 1055, 10.1074/mcp.M300054-MCP200
Huang, 2021, KinOrtho: A method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases, BMC Bioinformatics, 22, 446, 10.1186/s12859-021-04358-3
Jamieson, 2018, Substrate binding allosterically relieves autoinhibition of the pseudokinase TRIB1, Science Signaling, 11, eaau0597, 10.1126/scisignal.aau0597
Janson, 2021, PyMod 3: A complete suite for structural bioinformatics in PyMOL, Bioinformatics, 37, 1471, 10.1093/bioinformatics/btaa849
Jumper, 2021, Highly accurate protein structure prediction with AlphaFold, Nature, 596, 583, 10.1038/s41586-021-03819-2
Kannan, 2007, Structural and functional diversity of the microbial kinome, PLoS Biology, 5, 10.1371/journal.pbio.0050017
Khamrui, 2020, High-resolution structure and inhibition of the schizophrenia-linked Pseudokinase ULK4, Journal of the American Chemical Society, 142, 33, 10.1021/jacs.9b10458
Knighton, 1991, Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase, Science, 253, 407, 10.1126/science.1862342
Kullback, 1951, On information and sufficiency, The Annals of Mathematical Statistics, 22, 79, 10.1214/aoms/1177729694
Kwon, 2019, Tracing the origin and evolution of pseudokinases across the tree of life, Science Signaling, 12, eaav3810, 10.1126/scisignal.aav3810
Makarewicz, 2013, Molecular dynamics simulation by GROMACS using GUI plugin for PyMOL, Journal of Chemical Information and Modeling, 53, 1229, 10.1021/ci400071x
Manning, 2011, The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology, Genome Biology, 12, 1, 10.1186/gb-2011-12-7-r66
Manning, 2002, The protein kinase complement of the human genome, Science, 298, 1912, 10.1126/science.1075762
McSkimming, 2016, KinView: A visual comparative sequence analysis tool for integrated kinome research, Molecular BioSystems, 12, 3651, 10.1039/C6MB00466K
McSkimming, 2015, ProKinO: A unified resource for mining the cancer kinome, Human Mutation, 36, 175, 10.1002/humu.22726
Metz, 2018, Coral: Clear and customizable visualization of human Kinome data, Cell Systems, 7, 347, 10.1016/j.cels.2018.07.001
Morrison, 2006, Multiple sequence alignment for phylogenetic purposes, Australian Systematic Botany, 19, 479, 10.1071/SB06020
Murphy, 2015, Molecular mechanism of CCAAT-enhancer binding protein recruitment by the TRIB1 Pseudokinase, Structure, 23, 2111, 10.1016/j.str.2015.08.017
Murphy, 2014, A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties, Biochemical Journal, 457, 323, 10.1042/BJ20131174
Neuwald, 2009, Rapid detection, classification and accurate alignment of up to a million or more related protein sequences, Bioinformatics, 25, 1869, 10.1093/bioinformatics/btp342
Neuwald, 2011, Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms, Statistical Applications in Genetics and Molecular Biology, 10, 10.2202/1544-6115.1666
Neuwald, 2014, A Bayesian sampler for optimization of protein domain hierarchies, Journal of Computational Biology, 21, 269, 10.1089/cmb.2013.0099
Nichols, 2004, Characterization of three paralogous members of the mammalian vaccinia related kinase family, Journal of Biological Chemistry, 279, 7934, 10.1074/jbc.M310813200
Olson, 2019, A poxvirus pseudokinase represses viral DNA replication via a pathway antagonized by its paralog kinase, PLoS Pathogens, 15, 10.1371/journal.ppat.1007608
Park, 2015, Presumed pseudokinase VRK3 functions as a BAF kinase, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1853, 1738, 10.1016/j.bbamcr.2015.04.007
Pervez, 2014, Evaluating the accuracy and efficiency of multiple sequence alignment methods, Evolutionary Bioinformatics Online, 10, 205
Petrie, 2019, Viral MLKL homologs subvert necroptotic cell death by sequestering cellular RIPK3, Cell Reports, 28, 3309, 10.1016/j.celrep.2019.08.055
Preuss, 2020, Nucleotide binding, evolutionary insights, and interaction Partners of the Pseudokinase Unc-51-like kinase 4, Structure, 28, 1184, 10.1016/j.str.2020.07.016
Reiterer, 2014, Day of the dead: Pseudokinases and pseudophosphatases in physiology and disease, Trends in Cell Biology, 24, 489, 10.1016/j.tcb.2014.03.008
Ribeiro, 2018, Mechanism and catalytic site atlas (M-CSA): A database of enzyme reaction mechanisms and active sites, Nucleic Acids Research, 46, D618, 10.1093/nar/gkx1012
Ribeiro, 2020, Identifying pseudoenzymes using functional annotation: Pitfalls of common practice, The FEBS Journal, 287, 4128, 10.1111/febs.15142
Scheeff, 2009, Structure of the Pseudokinase VRK3 reveals a degraded catalytic site, a highly conserved kinase fold, and a putative regulatory binding site, Structure, 17, 128, 10.1016/j.str.2008.10.018
Schneider, 1990, Sequence logos: A new way to display consensus sequences, Nucleic Acids Research, 18, 6097, 10.1093/nar/18.20.6097
Schrödinger, 2019
Shrestha, 2020, Cataloguing the dead: Breathing new life into pseudokinase research, The FEBS Journal, 287, 4150, 10.1111/febs.15246
Talevich, 2013, Structural and evolutionary adaptation of rhoptry kinases and pseudokinases, a family of coccidian virulence factors, BMC Evolutionary Biology, 13, 1, 10.1186/1471-2148-13-117
Trott, 2010, AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, Journal of Computational Chemistry, 31, 455, 10.1002/jcc.21334
Tsuchiya, 2020, Covalent Aurora a regulation by the metabolic integrator coenzyme A, Redox Biology, 28, 10.1016/j.redox.2019.101318
Wang, 2020, Viral pseudoenzymes in infection and immunity, The FEBS Journal, 287, 4300, 10.1111/febs.15545
Ward, 2004, Protein kinases of the human malaria parasite plasmodium falciparum: The kinome of a divergent eukaryote, BMC Genomics, 5, 1, 10.1186/1471-2164-5-79
Watkins, 2017, ProtVista: Visualization of protein sequence annotations, Bioinformatics, 33, 2040, 10.1093/bioinformatics/btx120
Zaru, 2020, Challenges in the annotation of pseudoenzymes in databases: The UniProtKB approach, The FEBS Journal, 287, 4114, 10.1111/febs.15100
Zheng, 1993, 2.2 Å refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor, Acta Crystallographica Section D: Biological Crystallography, 49, 362, 10.1107/S0907444993000423