Bailey TL and C Elkan 1994 Fitting a mixture model by expectation maximization to discover motifs in bipolymers. ISMB-94 Proc. 1994 28–36
Bell E and Mullet JE 1991 Lipoxygenase gene expression is modulated in plants by water deficit, wounding, and methyl jasmonate. Molec. Gen. Genet. 230 456–462
Article PubMed CAS Google Scholar
Bell E and Mullet JE 1993 Characterization of an Arabidopsis lipoxygenase gene responsive to methyl jasmonate and wounding. Plant Physiol. 103 1133–1137
Chatonnet A, Perochon M, Velluet E, et al. 2023 The ESTHER database on alpha/beta hydrolase fold proteins – an overview of recent developments. Chem. Biol. Interact 13 110671
Desta IT, Porter KA, Xia B, et al. 2020 Performance and its limits in rigid body protein-protein docking. Structure 28 1071–1081
Article PubMed PubMed Central CAS Google Scholar
Domínguez-Solís JR, Gutiérrez-Alcalá G, Romero LC, et al. 2001 The cytosolic O-acetylserine (thiol) lyase gene is regulated by heavy metals and can function in cadmium tolerance. J. Biol. Chem. 276 9297–9302
Duhovny D, Nussinov R and Wolfson HJ 2002 Efficient unbound docking of rigid molecules; in Algorithms in Bioinformatics: Second International Workshop, WABI (Italy: Springer Berlin Heidelberg) pp 185–200
Fukao Y, Ferjani A, Fujiwara M, et al. 2009 Identification of zinc-responsive proteins in the roots of Arabidopsis thaliana using a highly improved method of two-dimensional electrophoresis. Plant Cell Physiol. 50 2234–2239
Article PubMed CAS Google Scholar
Gupta N, Kanojia A, Katiyar A, et al. 2021 Molecular characterization of NDL1-AGB1 mediated salt stress signaling: further exploration of the role of NDL1 interacting partners. Cells 10 2261
Article PubMed PubMed Central CAS Google Scholar
Holmquist M 2000 Alpha/Beta-hydrolase fold enzymes: structures, functions and mechanisms. Curr. Protein Pept. Sci. 1 209–235
Article PubMed CAS Google Scholar
Letunic I and Bork P 2021 Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49 293–296
Jakob K, Kniskern JM and Bergelson J 2007 The role of pectate lyase and the jasmonic acid defense response in Pseudomonas viridiflava virulence. Mol. Plant Microbe Interact. 20 146–158
Article PubMed CAS Google Scholar
Kanojia A and Mudgil Y 2020 Detailed in silico analysis of arabidopsis N-myc downregulated like (NDL) interactome with reference to stress sensing. Phytomorphology 70 87–104
Katiyar A and Mudgil Y 2019 Arabidopsis NDL-AGB1 modules play role in abiotic stress and hormonal responses along with their specific functions. IJMS 20 4736
Article PubMed PubMed Central CAS Google Scholar
Klopffleisch K, Phan N, Augustin K, et al. 2011 Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Mol. Syst. Biol. 7 532
Article PubMed PubMed Central Google Scholar
Koroleva OA, Calder G, Pendle AF, et al. 2009 Dynamic behavior of Arabidopsis eIF4A-III, putative core protein of exon junction complex: fast relocation to nucleolus and splicing speckles under hypoxia. Plant Cell 21 1592–1606
Article PubMed PubMed Central Google Scholar
Kozakov D, Beglov D, Bohnuud T, et al. 2013 How good is automated protein docking? Proteins 81 2159–2166
Kozakov D, Hall DR, Xia B, et al. 2017 The ClusPro web server for protein-protein docking. Nat. Protoc. 12 255–278
Article PubMed PubMed Central CAS Google Scholar
Kumar S, Stecher G and Tamura K 2016 MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33 1870–1874
Article PubMed PubMed Central CAS Google Scholar
Larkin MA, Blackshields G, Brown NP, et al. 2007 Clustal W and Clustal X version 2.0. Bioinformatics 2 2947–2948
Lee U, Wie C, Fernandez BO, et al. 2008 Modulation of nitrosative stress by S-nitrosoglutathione reductase is critical for thermotolerance and plant growth in Arabidopsis. Plant Cell 20 786–802
Article PubMed PubMed Central CAS Google Scholar
Mao Z, Sun J, Feng B, et al. 2013 The metastasis suppressor, N-myc downregulated gene 1 (NDRG1), is a prognostic biomarker for human colorectal cancer. PLoS One 8 e68206
Article PubMed PubMed Central CAS Google Scholar
Mawaribuchi S, Haramoto Y, Ikeda N, et al. 2023 Evolutionary features of ligands and their receptors via protein–protein interactions and essentiality in primates. Genes Cells 28 258–266
Article PubMed CAS Google Scholar
Melotte V, Qu X, Ongenaert M, et al. 2010 The N-myc downstream regulated gene (NDRG) family: diverse functions, multiple applications. FASEB J. 24 4153–4166
Article PubMed CAS Google Scholar
Mudgil Y, Ghawana S and Jones AM 2013 N-MYC down-regulated-like proteins regulate meristem initiation by modulating auxin transport and MAX2 expression. PLoS One 8 e77863
Article PubMed PubMed Central CAS Google Scholar
Mudgil Y, Uhrig JF, Zhou J, et al. 2009 Arabidopsis N-MYC DOWNREGULATED-LIKE1, a positive regulator of Auxin transport in a G protein–mediated pathway. Plant Cell 21 3591–3609
Article PubMed PubMed Central CAS Google Scholar
Ollis DL, Cheah E, Cygler M, et al. 1992 The α/β hydrolase fold. Protein Eng. 5 197–211
Pawson T and Nash P 2000 Protein–protein interactions define specificity in signal transduction. Genes Dev. 14 1027–1047
Article PubMed CAS Google Scholar
Pettersen EF, Goddard TD, Huang CC, et al. 2004 UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25 1605–1612
Article PubMed CAS Google Scholar
Rivera HE, Aichelman HE, Fifer JE, et al. 2021 A framework for understanding gene expression plasticity and its influence on stress tolerance. Mol. Ecol. 30 1381–1397
Article PubMed CAS Google Scholar
Schneidman-Duhovny D, Inbar Y, Nussinov R, et al. 2005 PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 33 363–367
Sedov IA and Zuev YF 2023 Recent advances in protein–protein. IJMS 24 1282
Article PubMed PubMed Central Google Scholar
Vajda S, Yueh C, Beglov D, et al. 2017 New additions to the ClusPro server motivated by CAPRI. Proteins Struct. Funct. Bioinf. 85 435–444
Varadi M, Bertoni D, Magana P, et al. 2024 AlphaFold protein structure database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res. 52 D368–D375
Comments (0)