How quickly can we predict trimethoprim resistance using alchemical free energy methods?

Reconciling the Potentially Irreconcilable? Genotypic and Phenotypic Amoxicillin-Clavulanate Resistance in Escherichia coli

(2020) Timothy J. Davies et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Ultrafast search of all deposited bacterial and viral genomic data

(2019) Phelim Bradley et al.   NATURE BIOTECHNOLOGY

Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches

(2019) Matteo Aldeghi et al.   ACS Central Science

Predicting Resistance Is (Not) Futile

(2019) Alice E. Brankin et al.   ACS Central Science

Uncertainty Quantification in Alchemical Free Energy Methods

(2018) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

(2018)   NEW ENGLAND JOURNAL OF MEDICINE

From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic

(2018) Francois Balloux et al.   TRENDS IN MICROBIOLOGY

Avoiding False Positive Conclusions in Molecular Simulation: The Importance of Replicas

(2018) Bernhard Knapp et al.   Journal of Chemical Theory and Computation

Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review

(2017) F. Tagini et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Tuberculosis is changing

(2017) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study

(2016) Louise J Pankhurst et al.   Lancet Respiratory Medicine

Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries

(2015) Elizabeth Jefferys et al.   Journal of Chemical Theory and Computation

Guidelines for the analysis of free energy calculations

(2015) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing

(2014) N. C. Gordon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

pmx: Automated protein structure and topology generation for alchemical perturbations

(2014) Vytautas Gapsys et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Platinum: a database of experimentally measured effects of mutations on structurally defined protein–ligand complexes

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

Prospective Screening of Novel Antibacterial Inhibitors of Dihydrofolate Reductase for Mutational Resistance

(2012) Kathleen M. Frey et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

(2012) Claudio U. Köser et al.   PLoS Pathogens

Predicting resistance mutations using protein design algorithms

(2010) K. M. Frey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Increased hydrophobic interactions of iclaprim with Staphylococcus aureus dihydrofolate reductase are responsible for the increase in affinity and antibacterial activity

(2009) C. Oefner et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY