4.6 Article

Proteome Exploration of Legionella pneumophila To Identify Novel Therapeutics: a Hierarchical Subtractive Genomics and Reverse Vaccinology Approach

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Infectious Diseases

Antimicrobial-induced horizontal transfer of antimicrobial resistance genes in bacteria: a mini-review

Gang Liu et al.

Summary: The emergence and spread of antimicrobial resistance among pathogenic bacteria pose a growing crisis for public health. Increased use and misuse of antimicrobials in medicine and livestock production have led to the selection of resistant bacteria. Horizontal gene transfer plays a crucial role in the spread of resistance genes. Antimicrobials not only have antibacterial effects but also stimulate horizontal gene transfer.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2022)

Article Biochemistry & Molecular Biology

Ensembl 2022

Fiona Cunningham et al.

Summary: Ensembl is unique in its flexible infrastructure for access to genomic data and annotation. They have focused on expediting annotation of new assemblies via the Ensembl Rapid Release platform, with the greatest annual number of newly annotated genomes released. They also developed a new method for comparative analyses and annotated non-vertebrate eukaryotes for the first time.

NUCLEIC ACIDS RESEARCH (2022)

Article Biotechnology & Applied Microbiology

The role of TolA, TolB, and TolR in cell morphology, OMVs production, and virulence of Salmonella Choleraesuis

Quan Li et al.

Summary: The Tol-Pal system is essential for maintaining outer membrane integrity in Gram-negative bacteria. Mutations in TolA, TolB, and TolR were found to cause severe damage to the cell wall, affecting the survival and virulence of Salmonella Choleraesuis. These proteins also play a role in outer membrane vesicles biogenesis, with potential implications for vaccination strategies.

AMB EXPRESS (2022)

Review Biochemistry & Molecular Biology

Molecular mechanisms and drivers of pathogen emergence

Deepak Balasubramanian et al.

Summary: This review emphasizes the diverse molecular and environmental drivers associated with pathogen emergence and highlights the roles of canonical gene transfer mechanisms and genetic variations. The authors contend that an integrated approach considering these factors is indispensable for a comprehensive understanding of and strategies to mitigate pathogen emergence.

TRENDS IN MICROBIOLOGY (2022)

Article Immunology

Roles of the Tol/Pal System in Bacterial Pathogenesis and Its Application to Antibacterial Therapy

Hidetada Hirakawa et al.

Summary: The Tol/Pal system is a set of protein complexes produced by Gram-negative bacteria, playing essential roles in colicin uptake, pathogenesis, and cell growth. It is proposed as a potential target for antimicrobial chemotherapy and vaccine development due to its immunogenicity and ability to stimulate immune responses.

VACCINES (2022)

Article Biochemical Research Methods

ToxinPred2: an improved method for predicting toxicity of proteins

Neelam Sharma et al.

Summary: The study presents ToxinPred2, a web-based tool for predicting the toxicity of proteins. Utilizing similarity, motif search, and machine-learning techniques, the tool achieves high accuracy in predicting protein toxicity. It is applicable to proteins from any source, making it a valuable resource in various research fields.

BRIEFINGS IN BIOINFORMATICS (2022)

Article Biochemistry & Molecular Biology

DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools

Hao Luo et al.

Summary: Essential genes are necessary for an organism's survival under specific conditions. Recent advancements in identifying human essential genes have been driven by the successful use of CRISPR/Cas9 technology. The release of DEG 15 database shows significant progress, with a large increase in the number of essential genes in eukaryotes and prokaryotes. The database offers built-in analysis modules and customizable BLAST tools for enhanced essential gene analysis.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemical Research Methods

AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes

Neelam Sharma et al.

Summary: AlgPred 2.0 is a web server developed for predicting allergenic proteins and regions in a protein, using various approaches and techniques for model training and validation, achieving high prediction accuracy.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biochemistry & Molecular Biology

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

Damian Szklarczyk et al.

Summary: The STRING database integrates various associations between proteins, including physical interactions and functional associations, by collecting evidence from sources such as literature, databases, computational predictions, and systematic transfers. STRING aims for wide coverage and provides extensive user interface features and querying methods for experimental data.

NUCLEIC ACIDS RESEARCH (2021)

Review Biochemistry & Molecular Biology

Natural transformation in Gram-negative bacteria thriving in extreme environments: from genes and genomes to proteins, structures and regulation

Beate Averhoff et al.

Summary: Extremophilic prokaryotes adapt to harsh environments through natural transformation, and horizontal gene transfer plays a crucial role in bacterial adaptation.

EXTREMOPHILES (2021)

Article Multidisciplinary Sciences

Immunoinformatics and molecular dynamics approaches: Next generation vaccine design against West Nile virus

Md Tahsin Khan et al.

Summary: In this study, an immunoinformatics approach was used to design a multi-epitope subunit vaccine against the West Nile Virus (WNV). The selected epitopes have shown strong immune response against WNV, suggesting they could be strong vaccine candidates to prevent WNV infections in humans. Further in vitro and in vivo investigations are needed to validate the potential of the vaccine candidate.

PLOS ONE (2021)

Article Microbiology

Subtractive Genomics Approach for Identification of Novel Therapeutic Drug Targets in Mycoplasma genitalium

Abiodun Joseph Fatoba et al.

Summary: This study aimed to identify novel drug targets against Mycoplasma genitalium infection by analyzing unique metabolic pathways and essential proteins. The research found seven potential druggable proteins involved in specific metabolic pathways of the pathogen, which could lead to the development of potent drugs for eradicating M. genitalium.

PATHOGENS (2021)

Article Infectious Diseases

Distribution of Legionella species and serogroups in patients with culture-confirmed Legionella pneumonia

Naoyuki Miyashita et al.

JOURNAL OF INFECTION AND CHEMOTHERAPY (2020)

Article Pathology

Legionnaires’ Disease: State of the Art Knowledge of Pathogenesis Mechanisms of Legionella

Sonia Mondino et al.

Annual Review of Pathology-Mechanisms of Disease (2019)

Article Biochemistry & Molecular Biology

DrugBank 5.0: a major update to the DrugBank database for 2018

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

PDBsum: Structural summaries of PDB entries

Roman A. Laskowski et al.

PROTEIN SCIENCE (2018)

Review Immunology

Factors Mediating Environmental Biofilm Formation by Legionella pneumophila

Arwa Abu Khweek et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2018)

Article Infectious Diseases

Immunoinformatics analysis and in silico designing of a novel multi-epitope peptide vaccine against Staphylococcus aureus

Nasim Hajighahramani et al.

INFECTION GENETICS AND EVOLUTION (2017)

Article Infectious Diseases

Macrolide resistance in Legionella pneumophila: the role of LpeAB efflux pump

Clemence Massip et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2017)

Review Medicine, Research & Experimental

Toll-like receptor 2 and its roles in immune responses against Legionella pneumophila

Shiva Ahmadishoar et al.

LIFE SCIENCES (2017)

Article Biochemistry & Molecular Biology

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes

Martin Closter Jespersen et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy

Yumeng Yan et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Public, Environmental & Occupational Health

Waterborne Disease Outbreaks Associated With Environmental and Undetermined Exposures to Water - United States, 2013-2014

R. Paul McClung et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2017)

Article Immunology

Weather-Dependent Risk for Legionnaires' Disease, United States

Jacob E. Simmering et al.

EMERGING INFECTIOUS DISEASES (2017)

Article Microbiology

Ribosomal Mutations Conferring Macrolide Resistance in Legionella pneumophilaO

Ghislaine Descours et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2017)

Article Multidisciplinary Sciences

Dynamics of genome change among Legionella species

Sandeep J. Joseph et al.

SCIENTIFIC REPORTS (2016)

Article Immunology

Identification of Novel Vaccine Candidates against Campylobacter through Reverse Vaccinology

Marine Meunier et al.

JOURNAL OF IMMUNOLOGY RESEARCH (2016)

Review Genetics & Heredity

Transfer of antibiotic-resistance genes via phage-related mobile elements

Maryury Brown-Jaque et al.

PLASMID (2015)

Article Biotechnology & Applied Microbiology

In silico design of a DNA-based HIV-1 multi-epitope vaccine for Chinese populations

Yi Yang et al.

HUMAN VACCINES & IMMUNOTHERAPEUTICS (2015)

Article Public, Environmental & Occupational Health

Surveillance for Waterborne Disease Outbreaks Associated with Drinking Water - United States, 2011-2012

Karlyn D. Beer et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2015)

Article Biochemical Research Methods

AllergenFP: allergenicity prediction by descriptor fingerprints

Ivan Dimitrov et al.

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

AllerTOP v.2-a server for in silico prediction of allergens

Ivan Dimitrov et al.

JOURNAL OF MOLECULAR MODELING (2014)

Review Infectious Diseases

Bacteriophage therapy: a potential solution for the antibiotic resistance crisis

Zhabiz Golkar et al.

JOURNAL OF INFECTION IN DEVELOPING COUNTRIES (2014)

Review Public, Environmental & Occupational Health

The antimicrobial resistance crisis: causes, consequences, and management

Carolyn Anne Michael et al.

FRONTIERS IN PUBLIC HEALTH (2014)

Article Biochemical Research Methods

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Sander Pronk et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology

Zuoshuang Xiang et al.

BMC BIOINFORMATICS (2013)

Article Biochemical Research Methods

Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins

Douglas B. Craig et al.

BMC BIOINFORMATICS (2013)

Article Immunology

Seven Ways to Preserve the Miracle of Antibiotics

John G. Bartlett et al.

CLINICAL INFECTIOUS DISEASES (2013)

Article Chemistry, Multidisciplinary

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

Jing Huang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)

Article Multidisciplinary Sciences

Use of Galleria mellonella as a Model Organism to Study Legionella pneumophila Infection

Clare R. Harding et al.

JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2013)

Article Multidisciplinary Sciences

A framework for human microbiome research

Barbara A. Methe et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

Immune epitope database analysis resource

Yohan Kim et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Infectious Diseases

Guidelines for the management of adult lower respiratory tract infections - Full version

M. Woodhead et al.

CLINICAL MICROBIOLOGY AND INFECTION (2011)

Article Chemistry, Medicinal

In Silico Subtractive Genomics for Target Identification in Human Bacterial Pathogens

Debmalya Barh et al.

DRUG DEVELOPMENT RESEARCH (2011)

Article Biochemistry & Molecular Biology

RaptorX: Exploiting structure information for protein alignment by statistical inference

Jian Peng et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)

Review Microbiology

Virulence properties of the Legionella pneumophila cell envelope

Olga Shevchuk et al.

FRONTIERS IN MICROBIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Caenorhabditis elegans as an Alternative Model Host for Legionella pneumophila, and Protective Effects of Bifidobacterium infantis

Tomomi Komura et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)

Article Biochemical Research Methods

CD-HIT Suite: a web server for clustering and comparing biological sequences

Ying Huang et al.

BIOINFORMATICS (2010)

Review Microbiology

Molecular Pathogenesis of Infections Caused by Legionella pneumophila

Hayley J. Newton et al.

CLINICAL MICROBIOLOGY REVIEWS (2010)

Review Genetics & Heredity

Genome-based approaches to vaccine development

Marirosa Mora et al.

JOURNAL OF MOLECULAR MEDICINE-JMM (2010)

Article Biotechnology & Applied Microbiology

How to improve R&D productivity: the pharmaceutical industry's grand challenge

Steven M. Paul et al.

NATURE REVIEWS DRUG DISCOVERY (2010)

Article Biochemistry & Molecular Biology

Allosteric β-propeller signalling in TolB and its manipulation by translocating colicins

Daniel A. Bonsor et al.

EMBO JOURNAL (2009)

Article Biochemistry & Molecular Biology

The NIH Human Microbiome Project

Jane Peterson et al.

GENOME RESEARCH (2009)

Article Immunology

OmpA of Uropathogenic Escherichia coli Promotes Postinvasion Pathogenesis of Cystitis

Tracy F. Nicholson et al.

INFECTION AND IMMUNITY (2009)

Article Infectious Diseases

Mutational paths towards increased fluoroquinolone resistance in Legionella pneumophila

Iyad Almahmoud et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2009)

Review Pharmacology & Pharmacy

Application of pharmacogenomics to vaccines

Gregory A. Poland et al.

PHARMACOGENOMICS (2009)

Article Biochemistry & Molecular Biology

KAAS: an automatic genome annotation and pathway reconstruction server

Yuki Moriya et al.

NUCLEIC ACIDS RESEARCH (2007)

Review Biotechnology & Applied Microbiology

More than one reason to rethink the use of peptides in vaccine design

Anthony W. Purcell et al.

NATURE REVIEWS DRUG DISCOVERY (2007)

Article Biochemical Research Methods

VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines

Irini A. Doytchinova et al.

BMC BIOINFORMATICS (2007)

Article Biochemical Research Methods

Predicting population coverage of T-cell epitope-based diagnostics and vaccines

Huynh-Hoa Bui et al.

BMC BIOINFORMATICS (2006)

Review Microbiology

A dynamic partnership: Celebrating our gut flora

CL Sears

ANAEROBE (2005)

Article Biochemistry & Molecular Biology

PatchDock and SymmDock: servers for rigid and symmetric docking

D Schneidman-Duhovny et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

JCat:: a novel tool to adapt codon usage of a target gene to its potential expression host

A Grote et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemical Research Methods

PSLpred: prediction of subcellular localization of bacterial proteins

M Bhasin et al.

BIOINFORMATICS (2005)

Article Multidisciplinary Sciences

The genomic sequence of the accidental pathogen Legionella pneumophila

MC Chien et al.

SCIENCE (2004)

Article Pharmacology & Pharmacy

Gemifloxacin: A new fluoroquinolone approved for treatment of respiratory infections

BK Yoo et al.

ANNALS OF PHARMACOTHERAPY (2004)

Article Microbiology

Improved methods for producing outer membrane vesicles in Gram-negative bacteria

T Henry et al.

RESEARCH IN MICROBIOLOGY (2004)

Article Biochemistry & Molecular Biology

ClusPro: a fully automated algorithm for protein-protein docking

SR Comeau et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

Structure validation by Cα geometry:: φ,ψ and Cβ deviation

SC Lovell et al.

PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)

Review Medicine, General & Internal

Gut flora in health and disease

F Guarner et al.

LANCET (2003)

Article Biochemistry & Molecular Biology

Naip5 affects host susceptibility to the intracellular pathogen Legionelia pneumophila

EK Wright et al.

CURRENT BIOLOGY (2003)

Review Microbiology

Legionella and Legionnaires' disease:: 25 years of investigation

BS Fields et al.

CLINICAL MICROBIOLOGY REVIEWS (2002)

Review Microbiology

Legionella pneumophila:: an aquatic microbe goes astray

M Steinert et al.

FEMS MICROBIOLOGY REVIEWS (2002)

Article Biochemistry & Molecular Biology

Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes

A Krogh et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)

Article Biotechnology & Applied Microbiology

TnAraOut, A transposon-based approach to identify and characterize essential bacterial genes

N Judson et al.

NATURE BIOTECHNOLOGY (2000)

Article Biochemical Research Methods

The PSIPRED protein structure prediction server

LJ McGuffin et al.

BIOINFORMATICS (2000)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)