In silico Prediction, Characterization, Molecular Docking, and Dynamic Studies on Fungal SDRs as Novel Targets for Searching Potential Fungicides Against Fusarium Wilt in Tomato

Predicting how drug molecules bind to their protein targets

(2018) Moira M Rachman et al.   CURRENT OPINION IN PHARMACOLOGY

Functional assignment for essential hypothetical proteins of Staphylococcus aureus N315

(2018) Jyoti Prava et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

(2018) Mohd Aamir et al.   PLoS One

A Novel Tomato Fusarium Wilt Tolerance Gene

(2018) Cahya Prihatna et al.   Frontiers in Microbiology

An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings

(2018) Irene Maffucci et al.   Frontiers in Chemistry

Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium oxysporum

(2017) Masaki Matsuoka et al.   Journal of Chemical Information and Modeling

FcRav2 , a gene with a ROGDI domain involved in Fusarium head blight and crown rot on durum wheat caused by Fusarium culmorum

(2017) Francesca Spanu et al.   MOLECULAR PLANT PATHOLOGY

Melanization of Fusarium keratoplasticum (F. solani Species Complex) During Disseminated Fusariosis in a Patient with Acute Leukemia

(2017) Siri Chiewchanvit et al.   MYCOPATHOLOGIA

Insight into resistance mechanisms of AZD4547 and E3810 to FGFR1 gatekeeper mutation via theoretical study

(2017) Donglou Liang et al.   Drug Design Development and Therapy

Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach

(2017) Mohd Aamir et al.   Frontiers in Plant Science

Molecular docking studies of 3-bromopyruvate and its derivatives to metabolic regulatory enzymes: Implication in designing of novel anticancer therapeutic strategies

(2017) Saveg Yadav et al.   PLoS One

ProTSAV: A protein tertiary structure analysis and validation server

(2016) Ankita Singh et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

(2016) Sayoni Das et al.   BIOINFORMATICS

In vitro and field efficacy of three fungicides against Fusarium bulb rot of garlic

(2016) Laura Gálvez Patón et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Antifungal activity of pomegranate peel extract against fusarium wilt of tomato

(2016) Domenico Rongai et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods

(2016) Xing Du et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Functional characterization of hypothetical proteins of Mycobacterium tuberculosis with possible esterase/lipase signature: a cumulative in silico and in vitro approach

(2016) Arbind Kumar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Inhibitor design against JNK1 through e-pharmacophore modeling docking and molecular dynamics simulations

(2016) Sudheer Kumar Katari et al.   JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION

Further Insights in the Binding Mode of Selective Inhibitors to Human PDE4D Enzyme Combining Docking and Molecular Dynamics

(2016) Pasqualina D'Ursi et al.   Molecular Informatics

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Efficacy of Bacillus spp. in the management of collar rot of Gerbera under protected cultivation

(2016) P. Suneeta et al.   RESEARCH ON CROPS

Black perithecial pigmentation in Fusarium species is due to the accumulation of 5-deoxybostrycoidin-based melanin

(2016) Rasmus J. N. Frandsen et al.   Scientific Reports

Molecular phylogeny, pathogenicity and toxigenicity of Fusarium oxysporum f. sp. lycopersici

(2016) D. Nirmaladevi et al.   Scientific Reports

Using plant essential oils to control Fusarium wilt in tomato plants

(2015) A. La Torre et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

An update to polyketide synthase and non-ribosomal synthetase genes and nomenclature in Fusarium

(2015) Frederik T. Hansen et al.   FUNGAL GENETICS AND BIOLOGY

In silico characterization of hypothetical proteins from Paracoccidioides lutzii

(2015) P.F.F. Silva et al.   GENETICS AND MOLECULAR RESEARCH

197 Combination of e-pharmacophore modeling, multiple docking strategies and molecular dynamic simulations to discover of novel antagonists of BACE1

(2015) Natarajan Pradeep et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Principal Component Analysis of Binding Energies for Single-Point Mutants of hT2R16 Bound to an Agonist Correlate with Experimental Mutant Cell Response

(2015) Derek E. Chen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Towards predictive docking at aminergic G-protein coupled receptors

(2015) Jan Jakubík et al.   JOURNAL OF MOLECULAR MODELING

Beware of docking!

(2015) Yu-Chian Chen   TRENDS IN PHARMACOLOGICAL SCIENCES

YASARA View—molecular graphics for all devices—from smartphones to workstations

(2014) Elmar Krieger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae

(2014) Dianguang Xiong et al.   BMC GENOMICS

Comparative Study on Sequence–Structure–Function Relationship of the Human Short-chain Dehydrogenases/Reductases Protein Family

(2014) Nu Thi Ngoc Tang et al.   Evolutionary Bioinformatics

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

(2014) David W. Wright et al.   Journal of Chemical Theory and Computation

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

CATH: comprehensive structural and functional annotations for genome sequences

(2014) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Plant defense response against Fusarium oxysporum and strategies to develop tolerant genotypes in banana

(2014) V. Swarupa et al.   PLANTA

CELLO2GO: A Web Server for Protein subCELlular LOcalization Prediction with Functional Gene Ontology Annotation

(2014) Chin-Sheng Yu et al.   PLoS One

Insilico analysis of hypothetical proteins unveils putative metabolic pathways and essential genes in Leishmania donovani

(2014) Nithin Ravooru et al.   Frontiers in Genetics

The history of tomato: From domestication to biopharming

(2013) Véronique Bergougnoux   BIOTECHNOLOGY ADVANCES

Homology Modeling, Docking Studies and Molecular Dynamic Simulations Using Graphical Processing Unit Architecture to Probe the Type-11 Phosphodiesterase Catalytic Site: A Computational Approach for the Rational Design of Selective Inhibitors

(2013) Elena Cichero et al.   Chemical Biology & Drug Design

On homology modeling of the M2 muscarinic acetylcholine receptor subtype

(2013) Jan Jakubík et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Expression patterns and regulation of SlCRF3 and SlCRF5 in response to cytokinin and abiotic stresses in tomato (Solanum lycopersicum)

(2013) Sarika Gupta et al.   JOURNAL OF PLANT PHYSIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Melanin Is Not Required for Turgor Generation but Enhances Cell-Wall Rigidity in Appressoria of the Corn Pathogen Colletotrichum graminicola

(2013) Nancy Ludwig et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Sanjeevini: a freely accessible web-server for target directed lead molecule discovery

(2012) B Jayaram et al.   BMC BIOINFORMATICS

Domain-mediated protein interaction prediction: From genome to network

(2012) Jüri Reimand et al.   FEBS LETTERS

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties

(2012) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations

(2012) Mingyun Shen et al.   Molecular BioSystems

An Efficient Computational Method for Calculating Ligand Binding Affinities

(2012) Atsushi Suenaga et al.   PLoS One

Fusarium oxysporum Adh1 has dual fermentative and oxidative functions and is involved in fungal virulence in tomato plants

(2011) Alma Rosa Corrales Escobosa et al.   FUNGAL GENETICS AND BIOLOGY

Functional analysis of the melanin biosynthesis genes ALM1 and BRM2-1 in the tomato pathotype of Alternaria alternata

(2011) Ahmed A. Kheder et al.   JOURNAL OF GENERAL PLANT PATHOLOGY

Structural and functional studies of a 50kDa antigenic protein from Salmonella enterica serovar Typhi

(2011) Yee Siew Choong et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Hybrid Steered Molecular Dynamics-Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target.

(2011) Katie L. Whalen et al.   Molecular Informatics

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Control of Fusarium wilt of tomato caused by Fusarium oxysporum f. sp. lycopersici using leaf extract of Piper betle L.: a preliminary study

(2011) Irom Manoj Singha et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Identification of Potential Leptospira Phosphoheptose Isomerase Inhibitors Through Virtual High-Throughput Screening

(2011) Amineni Umamaheswari et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Short-chain Dehydrogenase/reductase Gene is Required for Infection-related Development and Pathogenicity in Magnaporthe oryzae

(2010) Min-Jung Kwon et al.   Plant Pathology Journal

Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions

(2010) Nidhi Singh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

PROSITE, a protein domain database for functional characterization and annotation

(2009) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction

(2009) Bingding Huang   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

(2009) Kristoffer Illergård et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Eukaryotic Protein Domains as Functional Units of Cellular Evolution

(2009) J. Jin et al.   Science Signaling

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

(2009) Noriaki Okimoto et al.   PLoS Computational Biology

Medium- and short-chain dehydrogenase/reductase gene and protein families

(2008) K. L. Kavanagh et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Ligand Binding to the Voltage-Gated Kv1.5 Potassium Channel in the Open State—Docking and Computer Simulations of a Homology Model

(2007) Martin Andér et al.   BIOPHYSICAL JOURNAL