Mathematical model for plant-insect interaction with dynamic response to PAD4-BIK1 interaction and effect of BIK1 inhibition

Bent, 2007, Elicitors, effectors, and R genes: the new paradigm and a lifetime supply of questions, Annu. Rev. Phytopathol., 45, 399, 10.1146/annurev.phyto.45.062806.094427

Berendsen, 1995, Gromacs: a message-passing parallel molecular dynamics implementation, Comput. Phys. Commun., 91, 43, 10.1016/0010-4655(95)00042-E

Boller, 2009, A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors, Annu. Rev. Plant Biol., 60, 379, 10.1146/annurev.arplant.57.032905.105346

Bos, 2010, A functional genomics approach identifies candidate effectors from the aphid species Myzus persicae (green peach aphid), PLoS Genet., 6, 10.1371/journal.pgen.1001216

Clore, 1993, Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy, J. Mol. Biol., 231, 82, 10.1006/jmbi.1993.1259

Control Theory and, 2009

Danca, 1997, Detailed analysis of a nonlinear prey-predator model, J. Biol. Phys., 23, 11, 10.1023/A:1004918920121

De Vos, 2009, Myzus persicae (green peach aphid) salivary components induce defence responses in Arabidopsis thaliana, Plant Cell Environ., 32, 1548, 10.1111/j.1365-3040.2009.02019.x

Edelstein-Keshet, 1986, Mathematical theory for plant—herbivore systems, J. Math. Biol., 24, 25, 10.1007/BF00275719

Evans, 1991, A new 4th order runge-kutta method for initial value problems with error control, Int. J. Comput. Math., 39, 217, 10.1080/00207169108803994

Ferreira, 2015, Molecular docking and structure-based drug design strategies, Molecules, 20, 13384, 10.3390/molecules200713384

Fiser, 2010, 673, 73

Girousse, 2005, Aphid infestation causes different changes in carbon and nitrogen allocation in alfalfa stems as well as different inhibitions of longitudinal and radial expansion, Plant Physiol., 137, 1474, 10.1104/pp.104.057430

Hardin, 2002, Ab initio protein structure prediction, Curr. Opin. Struct. Biol., 12, 176, 10.1016/S0959-440X(02)00306-8

Huang, 2009, MetaPocket: a meta approach to improve protein ligand binding site prediction, Omics J. Integr. Biol., 13, 325, 10.1089/omi.2009.0045

Jirage, 1999, Arabidopsis thaliana PAD4 encodes a lipase-like gene that is important for salicylic acid signaling, Proc. Natl. Acad. Sci. U. S. A., 96, 13583, 10.1073/pnas.96.23.13583

Kartal, 2016, Dynamics of a plant herbivore model with differential difference equations, Cogent Math., 3, 10.1080/23311835.2015.1136198

Kelley, 2015, The Phyre2 web portal for protein modeling, prediction and analysis, Nat. Protoc., 10, 845, 10.1038/nprot.2015.053

Kettles, 2013, Resistance of Arabidopsis thaliana to the green peach aphid, Myzus persicae, involves camalexin and is regulated by microRNAs, New Phytol., 198, 1178, 10.1111/nph.12218

Lei, 2014, Botrytis-induced kinase1 modulates Arabidopsis resistance to green peach aphids via phytoalexin deficient4, Plant Physiol., 165, 1657, 10.1104/pp.114.242206

Letunic, 2015, Smart: recent updates, new developments and status in 2015, Nucleic Acids Res., 43, D257, 10.1093/nar/gku949

Louis, 2015, Plant defence against aphids: the PAD4 signalling nexus, J. Exp. Bot., 66, 449, 10.1093/jxb/eru454

Louis, 2010, PAD4 -Dependent antibiosis contributes to the ssi2 -Conferred hyper-resistance to the green peach Aphid, Mol. Plant Microbe Interact., 23, 618, 10.1094/MPMI-23-5-0618

Louis, 2012, Discrimination of Arabidopsis PAD4 activities in defense against green peach aphid and pathogens, Plant Physiol., 158, 1860, 10.1104/pp.112.193417

Lovell, 2003, Structure validation by Calpha geometry: phi,psi and Cbeta deviation, Proteins, 50, 437, 10.1002/prot.10286

Lu, 2010, A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity, Proc. Natl. Acad. Sci., 107, 496, 10.1073/pnas.0909705107

Mantelin, 2009, Ethylene contributes to potato aphid susceptibility in a compatible tomato host, New Phytol., 183, 444, 10.1111/j.1469-8137.2009.02870.x

Marchler-Bauer, 2017, CDD/Sparcle: functional classification of proteins via subfamily domain architectures, Nucleic Acids Res., 45, D200, 10.1093/nar/gkw1129

May, 2001

Nguyen, 2016, Chalcone-based selective inhibitors of a C4 plant key enzyme as novel potential herbicides, Sci. Rep., 6, 10.1038/srep27333

Pegadaraju, 2007, Phloem-based resistance to green peach aphid is controlled by Arabidopsis phytoalexin deficient4 without its signaling partner enhanced disease susceptibility1, Plant J. Cell Mol. Biol., 52, 332, 10.1111/j.1365-313X.2007.03241.x

Pegadaraju, 2005, Premature leaf senescence modulated by the Arabidopsis phytoalexin deficient4 gene is associated with defense against the phloem-feeding green peach Aphid, Plant Physiol., 139, 1927, 10.1104/pp.105.070433

Prince, 2014, The leucine-rich repeat receptor-like kinase brassinosteroid insensitive1-associated kinase1 and the cytochrome P450 phytoalexin deficient3 contribute to innate immunity to aphids in arabidopsis, Plant Physiol., 164, 2207, 10.1104/pp.114.235598

Schüttelkopf, 2004, Prodrg: a tool for high-throughput crystallography of protein-ligand complexes, Acta Crystallogr. D Biol. Crystallogr., 60, 1355, 10.1107/S0907444904011679

Scott, 1999, The Gromos biomolecular simulation program package, J. Phys. Chem. A, 103, 3596, 10.1021/jp984217f

Sigrist, 2010, Prosite, a protein domain database for functional characterization and annotation, Nucleic Acids Res., 38, D161, 10.1093/nar/gkp885

Stieha, 2016, The effects of plant compensatory regrowth and induced resistance on herbivore population dynamics, Am. Nat., 187, 167, 10.1086/684522

Thompson, 2006, Transcriptomics and functional genomics of plant defence induction by phloem-feeding insects, J. Exp. Bot., 57, 755, 10.1093/jxb/erj135

Tjallingii, 2006, Salivary secretions by aphids interacting with proteins of phloem wound responses, J. Exp. Bot., 57, 739, 10.1093/jxb/erj088

Volkamer, 2012, Combining global and local measures for structure-based druggability predictions, J. Chem. Inf. Model., 52, 360, 10.1021/ci200454v

Will, 2006, Physical and chemical interactions between aphids and plants, J. Exp. Bot., 57, 729, 10.1093/jxb/erj089

Zhang, 2011, Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling, Structure, 19, 1784, 10.1016/j.str.2011.09.022