Virtual screening of natural ligands from five resources to target Ralstonia solanacearum polygalacturonase and endoglucanase

[1]  Vijay Kumar Bhardwaj,et al.  Structure restoration and aggregate inhibition of V30M mutant transthyretin protein by potential quinoline molecules. , 2023, International journal of biological macromolecules.

[2]  Rahul Singh,et al.  Computational analysis of protein-ligand interaction by targeting a cell cycle restrainer , 2023, Comput. Methods Programs Biomed..

[3]  Silvio C. E. Tosatto,et al.  InterPro in 2022 , 2022, Nucleic Acids Res..

[4]  G. Horváth,et al.  Antibacterial Effect of Lemongrass (Cymbopogon citratus) against the Aetiological Agents of Pitted Keratolyis , 2022, Molecules.

[5]  M. Elashtokhy,et al.  Bactericidal activity of some plant essential oils against Ralstonia solanacearum infection , 2021, Saudi journal of biological sciences.

[6]  Mohamed S. Sedeek,et al.  Antifungal Evaluation and Molecular Docking Studies of Olea europaea Leaf Extract, Thymus vulgaris and Boswellia carteri Essential Oil as Prospective Fungal Inhibitor Candidates , 2021, Molecules.

[7]  R. Eswaramoorthy,et al.  Molecular docking analysis and evaluation of the antibacterial and antioxidant activities of the constituents of Ocimum cufodontii , 2021, Scientific Reports.

[8]  Benjamin A. Shoemaker,et al.  PubChem in 2021: new data content and improved web interfaces , 2020, Nucleic Acids Res..

[9]  Vijay Kumar Bhardwaj,et al.  Identification of novel and selective agonists for ABA receptor PYL3. , 2020, Plant physiology and biochemistry : PPB.

[10]  K. Lai,et al.  Terpene Derivatives as a Potential Agent against Antimicrobial Resistance (AMR) Pathogens , 2019, Molecules.

[11]  Seungdon Lee,et al.  Prediction of Host-Specific Genes by Pan-Genome Analyses of the Korean Ralstonia solanacearum Species Complex , 2019, Front. Microbiol..

[12]  Bertrand Caron,et al.  Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane. , 2018, Journal of chemical theory and computation.

[13]  C. Faustino,et al.  Rosmarinus officinalis L.: an update review of its phytochemistry and biological activity , 2018, Future science OA.

[14]  M. Govarthanan,et al.  Cellulase enzyme: Homology modeling, binding site identification and molecular docking , 2017 .

[15]  Olivier Michielin,et al.  SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules , 2017, Scientific Reports.

[16]  R. Pathak,et al.  Molecular modeling and docking studies of phytoalexin(s) with pathogenic protein(s) as molecular targets for designing the derivatives with anti-fungal action on Alternaria spp. of Brassica , 2016 .

[17]  Henrique Douglas Melo Coutinho,et al.  Ocimum basilicum: Antibacterial activity and association study with antibiotics against bacteria of clinical importance , 2016, Pharmaceutical biology.

[18]  W. Raza,et al.  Response of tomato wilt pathogen Ralstonia solanacearum to the volatile organic compounds produced by a biocontrol strain Bacillus amyloliquefaciens SQR-9 , 2016, Scientific Reports.

[19]  P. Liu,et al.  Resistance Mechanisms and Molecular Docking Studies of Four Novel QoI Fungicides in Peronophythora litchii , 2015, Scientific Reports.

[20]  David Taylor,et al.  The Pharmaceutical Industry and the Future of Drug Development , 2015 .

[21]  Dima Kozakov,et al.  The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins , 2015, Nature Protocols.

[22]  H. Kong,et al.  Induction of the Viable but Nonculturable State of Ralstonia solanacearum by Low Temperature in the Soil Microcosm and Its Resuscitation by Catalase , 2014, PloS one.

[23]  K. RaviVital,et al.  Review on Thymus vulgaris Traditional Uses and Pharmacological Properties , 2014 .

[24]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[25]  R. Coppola,et al.  Effect of Essential Oils on Pathogenic Bacteria , 2013, Pharmaceuticals.

[26]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[27]  Pramod C. Nair,et al.  An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. , 2011, Journal of chemical theory and computation.

[28]  Jason C. Hong,et al.  Management of bacterial wilt in tomatoes with thymol and acibenzolar-S-methyl , 2011 .

[29]  A. Pich,et al.  Endo- and exopolygalacturonases of Ralstonia solanacearum are inhibited by polygalacturonase-inhibiting protein (PGIP) activity in tomato stem extracts. , 2011, Plant physiology and biochemistry : PPB.

[30]  I. Bassolé,et al.  Composition and Antimicrobial Activities of Lippia multiflora Moldenke, Mentha x piperita L. and Ocimum basilicum L. Essential Oils and Their Major Monoterpene Alcohols Alone and in Combination , 2010, Molecules.

[31]  M. Paret,et al.  Effect of Plant Essential Oils on Ralstonia solanacearum Race 4 and Bacterial Wilt of Edible Ginger. , 2010, Plant disease.

[32]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[33]  M. López,et al.  PCR DETECTION AND IDENTIFICATION OF PLANT-PATHOGENIC BACTERIA: UPDATED REVIEW OF PROTOCOLS (1989-2007) , 2009 .

[34]  L. Berti,et al.  Geraniol Restores Antibiotic Activities against Multidrug-Resistant Isolates from Gram-Negative Species , 2009, Antimicrobial Agents and Chemotherapy.

[35]  N. Mimica-Dukić,et al.  Antimicrobial and antioxidant properties of rosemary and sage (Rosmarinus officinalis L. and Salvia officinalis L., Lamiaceae) essential oils. , 2007, Journal of agricultural and food chemistry.

[36]  Daciana Ciocan,et al.  PLANT PRODUCTS AS ANTIMICROBIAL AGENTS , 2007 .

[37]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[38]  M. Schell,et al.  Pyramiding unmarked deletions in Ralstonia solanacearum shows that secreted proteins in addition to plant cell-wall-degrading enzymes contribute to virulence. , 2005, Molecular plant-microbe interactions : MPMI.

[39]  Matthias Adam,et al.  Integrating research and development: the emergence of rational drug design in the pharmaceutical industry. , 2005, Studies in history and philosophy of biological and biomedical sciences.

[40]  Francesco Castelli,et al.  Mechanisms of Antibacterial Action of Three Monoterpenes , 2005, Antimicrobial Agents and Chemotherapy.

[41]  S. Roller,et al.  Antimicrobial Action of Carvacrol at Different Stages of Dual-Species Biofilm Development by Staphylococcus aureus and Salmonella enterica Serovar Typhimurium , 2005, Applied and Environmental Microbiology.

[42]  M. Mahomoodally,et al.  Antimicrobial Activities and Phytochemical Profiles of Endemic Medicinal Plants of Mauritius , 2005 .

[43]  F. Senatore,et al.  Antibacterial activity of Coriandrum sativum L. and Foeniculum vulgare Miller Var. vulgare (Miller) essential oils. , 2004, Journal of agricultural and food chemistry.

[44]  J. D. van Elsas,et al.  The Low-Temperature-Induced Viable-But-Nonculturable State Affects the Virulence of Ralstonia solanacearum Biovar 2. , 2004, Phytopathology.

[45]  M. Polissiou,et al.  The effectiveness of plant essential oils on the growth of Botrytis cinerea, Fusarium sp. and Clavibacter michiganensis subsp. michiganensis , 2003 .

[46]  Zurich,et al.  Predicting crystal structures: the Parrinello-Rahman method revisited. , 2002, Physical review letters.

[47]  Jiang Xiaohua,et al.  Three dimentional quantitative structure-activity relationships of novel 2-heteroaryl-4-chromanone derivatives , 2002 .

[48]  T. R. Steck,et al.  The Viable But Nonculturable State ofRalstonia solanacearum May Be Involved in Long-Term Survival and Plant Infection , 2001, Applied and Environmental Microbiology.

[49]  G. G. Nascimento,et al.  Antibacterial activity of plant extracts and phytochemicals on antibiotic-resistant bacteria , 2000 .

[50]  S. Wyllie,et al.  The role of structure and molecular properties of terpenoids in determining their antimicrobial activity. , 1999 .

[51]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[52]  J M Thornton,et al.  LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. , 1995, Protein engineering.

[53]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

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

[55]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[56]  M. Kimura A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[57]  Vijay Kumar Bhardwaj,et al.  New ecdysone receptor agonists: a computational approach for rational discovery of insecticides for crop protection , 2021, Molecular Systems Design & Engineering.

[58]  Shahalam Khan,et al.  Chemical composition, in vitro antibacterial and antioxidant potential of Omani Thyme essential oil along with in silico studies of its major constituent , 2020 .

[59]  S. Genin,et al.  Pathogenomics of the Ralstonia solanacearum species complex. , 2012, Annual review of phytopathology.