Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages

Structure guided prediction of Pyrazinamide resistance mutations in pncA

(2020) Malancha Karmakar et al.   Scientific Reports

Pyrazinamide triggers degradation of its target aspartate decarboxylase

(2020) Pooja Gopal et al.   Nature Communications

Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: Evidence for coevolution?

(2020) Michael L. McHenry et al.   PLoS Genetics

Identification of pathogenic missense mutations using protein stability predictors

(2020) Lukas Gerasimavicius et al.   Scientific Reports

Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies

(2020) Gary Napier et al.   Genome Medicine

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks

(2019) Huali Cao et al.   Journal of Chemical Information and Modeling

Pyrazinamide resistance and mutations in pncA among isolates of Mycobacterium tuberculosis from Khyber Pakhtunkhwa, Pakistan

(2019) Muhammad Tahir khan et al.   BMC INFECTIOUS DISEASES

Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance

(2019) Yaa E. A. Oppong et al.   BMC GENOMICS

Stepwise acquisition of rv0678 and atpE mutations conferring bedaquiline resistance: an in vitro study

(2019) Nabila Ismail et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

mCSM-PPI2: predicting the effects of mutations on protein–protein interactions

(2019) Carlos H M Rodrigues et al.   NUCLEIC ACIDS RESEARCH

The Interplay of Human and Mycobacterium Tuberculosis Genomic Variability

(2019) Wilian Correa-Macedo et al.   Frontiers in Genetics

Structural Dynamics Behind Clinical Mutants of PncA-Asp12Ala, Pro54Leu, and His57Pro of Mycobacterium tuberculosis Associated With Pyrazinamide Resistance

(2019) Aamir Mehmood et al.   Frontiers in Bioengineering and Biotechnology

Analysis of a Novel pncA Mutation for Susceptibility to Pyrazinamide Therapy

(2018) Malancha Karmakar et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

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

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

(2018) Francesc Coll et al.   NATURE GENETICS

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

(2018) Carlos HM Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis

(2018) Stephanie Portelli et al.   Scientific Reports

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

(2018) Erol S. Kavvas et al.   Nature Communications

Non- pncA Gene-Mutated but Pyrazinamide-Resistant Mycobacterium tuberculosis: Why Is That?

(2017) Jim Werngren et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures

(2017) Harry C Jubb et al.   JOURNAL OF MOLECULAR BIOLOGY

SDM: a server for predicting effects of mutations on protein stability

(2017) Arun Prasad Pandurangan et al.   NUCLEIC ACIDS RESEARCH

mCSM–NA: predicting the effects of mutations on protein–nucleic acids interactions

(2017) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

Epistasis and the Evolution of Antimicrobial Resistance

(2017) Alex Wong   Frontiers in Microbiology

Diversity and evolution of drug resistance mechanisms in Mycobacterium tuberculosis

(2017) Mashael Al-Saeedi et al.   Infection and Drug Resistance

INPS-MD: a web server to predict stability of protein variants from sequence and structure: Table 1.

(2016) Castrense Savojardo et al.   BIOINFORMATICS

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

(2016) Jody Phelan et al.   BMC Medicine

Molecular principles behind pyrazinamide resistance due to mutations in panD gene in Mycobacterium tuberculosis

(2016) Bharati Pandey et al.   GENE

mCSM-AB: a web server for predicting antibody–antigen affinity changes upon mutation with graph-based signatures

(2016) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

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

Pyrazinamide Resistance Is Caused by Two Distinct Mechanisms: Prevention of Coenzyme A Depletion and Loss of Virulence Factor Synthesis

(2016) Pooja Gopal et al.   ACS Infectious Diseases

A Global Perspective on Pyrazinamide Resistance: Systematic Review and Meta-Analysis

(2015) Michael G. Whitfield et al.   PLoS One

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

(2014) D. E. V. Pires et al.   NUCLEIC ACIDS RESEARCH

A series of PDB-related databanks for everyday needs

(2014) Wouter G. Touw et al.   NUCLEIC ACIDS RESEARCH

Mycobacterium tuberculosis Pyrazinamide Resistance Determinants: a Multicenter Study

(2014) P. Miotto et al.   mBio

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

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

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

Drug resistance mechanism of PncA inMycobacterium tuberculosis

(2013) Vidya Rajendran et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Role of pncA and rpsA Gene Sequencing in Detection of Pyrazinamide Resistance in Mycobacterium tuberculosis Isolates from Southern China

(2013) Y. Tan et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis

(2013) Christopher B Ford et al.   NATURE GENETICS

Clade-Specific Virulence Patterns of Mycobacterium tuberculosis Complex Strains in Human Primary Macrophages and Aerogenically Infected Mice

(2013) N. Reiling et al.   mBio

Systematic Analysis of Pyrazinamide-Resistant Spontaneous Mutants and Clinical Isolates of Mycobacterium tuberculosis

(2012) Karolien Stoffels et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

New Mutations in the Mycobacterial ATP Synthase: New Insights into the Binding of the Diarylquinoline TMC207 to the ATP Synthase C-Ring Structure

(2012) Elena Segala et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Putative Compensatory Mutations in the rpoC Gene of Rifampin-Resistant Mycobacterium tuberculosis Are Associated with Ongoing Transmission

(2012) M. de Vos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Gene Sequencing for Routine Verification of Pyrazinamide Resistance in Mycobacterium tuberculosis: a Role for pncA but Not rpsA

(2012) D. C. Alexander et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Role ofrpsAGene Sequencing in Diagnosis of Pyrazinamide Resistance: Table 1

(2012) Sami O. Simons et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

ExPASy: SIB bioinformatics resource portal

(2012) P. Artimo et al.   NUCLEIC ACIDS RESEARCH

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

(2011) Iñaki Comas et al.   NATURE GENETICS

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

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

Crystal Structure of the Pyrazinamidase of Mycobacterium tuberculosis: Insights into Natural and Acquired Resistance to Pyrazinamide

(2011) Stéphanie Petrella et al.   PLoS One

A biophysical protein folding model accounts for most mutational fitness effects in viruses

(2011) C. S. Wylie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pyrazinamide Inhibits Trans-Translation in Mycobacterium tuberculosis

(2011) W. Shi et al.   SCIENCE

Genotypic analysis of genes associated with isoniazid and ethionamide resistance in MDR-TB isolates from Thailand

(2009) S. Boonaiam et al.   CLINICAL MICROBIOLOGY AND INFECTION

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY