Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions

(2018) Erol S. Kavvas et al.   BMC Systems Biology

Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care

(2018) Navisha Dookie et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Molecular epidemiology of multi- and extensively-drug-resistant Mycobacterium tuberculosis in Ireland, 2001–2014

(2018) E. Roycroft et al.   JOURNAL OF INFECTION

Drug-resistant tuberculosis: the rise of the monos

(2018) Ebrahim Variava et al.   LANCET INFECTIOUS DISEASES

Drug-resistant tuberculosis: An update on disease burden, diagnosis and treatment

(2018) Christoph Lange et al.   RESPIROLOGY

The Search for ‘Evolution-Proof’ Antibiotics

(2018) Graham Bell et al.   TRENDS IN MICROBIOLOGY

Phylogenomics and antimicrobial resistance of the leprosy bacillus Mycobacterium leprae

(2018) Andrej Benjak et al.   Nature Communications

Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae

(2018) Sundeep Chaitanya Vedithi et al.   Scientific Reports

Nontuberculous mycobacterial pulmonary disease: an increasing burden with substantial costs

(2017) D. Rebecca Prevots et al.   EUROPEAN RESPIRATORY JOURNAL

Rapid detection of mutations in erm (41) and rrl associated with clarithromycin resistance in Mycobacterium abscessus complex by denaturing gradient gel electrophoresis

(2017) Weijia Liu et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections

(2017) Sherine E. Thomas et al.   JOURNAL OF MOLECULAR BIOLOGY

Comparative genome analyses of mycobacteria give better insights into their evolution

(2017) Wei Yee Wee et al.   PLoS One

Critical assessment of methods of protein structure prediction (CASP)-Round XII

(2017) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis

(2017) Michael A. DeJesus et al.   mBio

Decoding the similarities and differences among mycobacterial species

(2017) Sony Malhotra et al.   PLoS Neglected Tropical Diseases

Genomic Comparisons Reveal Microevolutionary Differences in Mycobacterium abscessus Subspecies

(2017) Joon L. Tan et al.   Frontiers in Microbiology

A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes

(2017) Chong Peng et al.   Frontiers in Microbiology

Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach

(2017) Grace Mugumbate et al.   Frontiers in Pharmacology

Protein crystallography and drug discovery: recollections of knowledge exchange between academia and industry

(2017) Tom L. Blundell   IUCrJ

Genetic diversity, transmission dynamics and drug resistance of Mycobacterium tuberculosis in Angola

(2017) João Perdigão et al.   Scientific Reports

Data Intensive Genome Level Analysis for Identifying Novel, Non-Toxic Drug Targets for Multi Drug Resistant Mycobacterium tuberculosis

(2017) Divneet Kaur et al.   Scientific Reports

Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications

(2016) Guillaume Sapriel et al.   BMC GENOMICS

Drug-resistant M leprae

(2016) Paul R. Saunderson   CLINICS IN DERMATOLOGY

Update on pulmonary disease due to non-tuberculous mycobacteria

(2016) Jason E. Stout et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Mycobacterial Taxonomy

(2016) Betty A. Forbes   JOURNAL OF CLINICAL MICROBIOLOGY

Virtual Screening and X-ray Crystallography Identify Non-Substrate Analog Inhibitors of Flavin-Dependent Thymidylate Synthase

(2016) Rosaria Luciani et al.   JOURNAL OF MEDICINAL CHEMISTRY

Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors

(2016) Madeline E. Kavanagh et al.   JOURNAL OF MEDICINAL CHEMISTRY

Identifying Interactions that Determine Fragment Binding at Protein Hotspots

(2016) Chris J. Radoux et al.   JOURNAL OF MEDICINAL CHEMISTRY

Computational identification of potential drug targets against Mycobacterium leprae

(2016) Reaz Uddin et al.   MEDICINAL CHEMISTRY RESEARCH

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines

(2016) Wei-Hua Chen et al.   NUCLEIC ACIDS RESEARCH

Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium

(2016) Josephine M. Bryant et al.   SCIENCE

mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance

(2016) Douglas E. V. Pires et al.   Scientific Reports

The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis

(2016) Vinayak Singh et al.   ACS Infectious Diseases

In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity

(2016) Douglas E. V. Pires et al.   Scientific Reports

Optimization of Inhibitors ofMycobacterium tuberculosisPantothenate Synthetase Based on Group Efficiency Analysis

(2015) Alvin W. Hung et al.   ChemMedChem

The future for early-stage tuberculosis drug discovery

(2015) Edison S Zuniga et al.   Future Microbiology

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability

(2015) Vincent Frappier et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

(2015) Keira A. Cohen et al.   PLOS MEDICINE

Genome analysis reveals three genomospecies in Mycobacterium abscessus

(2014) Mohamed Sassi et al.   BMC GENOMICS

Structure-Guided Design of Thiazolidine Derivatives asMycobacterium tuberculosisPantothenate Synthetase Inhibitors

(2014) Parthiban Brindha Devi et al.   ChemMedChem

Three-dimensional protein structure prediction: Methods and computational strategies

(2014) Márcio Dorn et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Molecular surveillance of multi- and extensively drug-resistant tuberculosis transmission in the European Union from 2003 to 2011

(2014) J L De Beer et al.   Eurosurveillance

Genome Sequencing of Mycobacterium abscessus Isolates from Patients in the United States and Comparisons to Globally Diverse Clinical Strains

(2014) R. M. Davidson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Structure Guided Lead Generation for M. tuberculosis Thymidylate Kinase (Mtb TMK): Discovery of 3-Cyanopyridone and 1,6-Naphthyridin-2-one as Potent Inhibitors

(2014) Maruti Naik et al.   JOURNAL OF MEDICINAL CHEMISTRY

Diversity and Evolution of Mycobacterium tuberculosis: Moving to Whole-Genome-Based Approaches

(2014) S. Niemann et al.   Cold Spring Harbor Perspectives in Medicine

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

The evolutionary rate of antibacterial drug targets

(2013) Arkadiusz Gladki et al.   BMC BIOINFORMATICS

A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis

(2013) Soma Ghosh et al.   BMC Systems Biology

Structure-Guided Design of Novel Thiazolidine Inhibitors of O-Acetyl Serine Sulfhydrylase from Mycobacterium tuberculosis

(2013) Ömer Poyraz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat et al.   NATURE GENETICS

Identification and Characterization of Potential Therapeutic Candidates in Emerging Human Pathogen Mycobacterium abscessus: A Novel Hierarchical In Silico Approach

(2013) Buvaneswari Shanmugham et al.   PLoS One

Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients

(2013) Matthias Merker et al.   PLoS One

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Metabolomics Reveal d-Alanine:d-Alanine Ligase As the Target of d-Cycloserine in Mycobacterium tuberculosis

(2013) Gareth A. Prosser et al.   ACS Medicinal Chemistry Letters

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

(2013) Andreas Roetzer et al.   PLOS MEDICINE

Pathway-Selective Sensitization of Mycobacterium tuberculosis for Target-Based Whole-Cell Screening

(2012) Garth L. Abrahams et al.   CHEMISTRY & BIOLOGY

Mycobacterium abscessus: a new antibiotic nightmare

(2012) R. Nessar et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Challenges of Antibacterial Discovery

(2011) L. L. Silver   CLINICAL MICROBIOLOGY REVIEWS

DNA fingerprinting of Mycobacterium tuberculosis: From phage typing to whole-genome sequencing

(2011) Anita C. Schürch et al.   INFECTION GENETICS AND EVOLUTION

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism

(2011) Jennifer E. Griffin et al.   PLoS Pathogens

Mycobacterium leprae: genes, pseudogenes and genetic diversity

(2010) Pushpendra Singh et al.   Future Microbiology

Origins and Evolution of Antibiotic Resistance

(2010) J. Davies et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Comparative genomic and phylogeographic analysis of Mycobacterium leprae

(2009) Marc Monot et al.   NATURE GENETICS

Non Mycobacterial Virulence Genes in the Genome of the Emerging Pathogen Mycobacterium abscessus

(2009) Fabienne Ripoll et al.   PLoS One

Structural bioinformatics mutation analysis reveals genotype-phenotype correlations in von Hippel-Lindau disease and suggests molecular mechanisms of tumorigenesis

(2009) Julia R. Forman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS