The application of machine learning techniques to innovative antibacterial discovery and development

A Deep Learning Approach to Antibiotic Discovery

(2020) Jonathan M. Stokes et al.   CELL

Machine intelligence in peptide therapeutics: A next‐generation tool for rapid disease screening

(2020) Shaherin Basith et al.   MEDICINAL RESEARCH REVIEWS

Methicillin-resistant Staphylococcus aureus: an overview of basic and clinical research

(2019) Nicholas A. Turner et al.   NATURE REVIEWS MICROBIOLOGY

The Concept of an Ideal Antibiotic: Implications for Drug Design

(2019) Márió Gajdács   MOLECULES

Alternatives to Conventional Antibiotics in the Era of Antimicrobial Resistance

(2019) Chandradhish Ghosh et al.   TRENDS IN MICROBIOLOGY

Machine Learning Techniques to Identify Antimicrobial Resistance in the Intensive Care Unit

(2019) Sergio Martínez-Agüero et al.   Entropy

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data

(2019) Allison L. Hicks et al.   PLoS Computational Biology

Identification of Novel Antibacterials Using Machine Learning Techniques

(2019) Yan A. Ivanenkov et al.   Frontiers in Pharmacology

Virtual screening of antibacterial compounds by similarity search of Enoyl-ACP reductase (FabI) inhibitors

(2019) Leonardo Rander Asse Junior et al.   Future Medicinal Chemistry

Recent updates on drug resistance in Mycobacterium tuberculosis

(2019) R. Singh et al.   JOURNAL OF APPLIED MICROBIOLOGY

AntiBac-Pred: A Web Application for Predicting Antibacterial Activity of Chemical Compounds

(2019) Pavel V. Pogodin et al.   Journal of Chemical Information and Modeling

Recent applications of machine learning in medicinal chemistry

(2018) Jane Panteleev et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

In silico identification, synthesis and biological evaluation of novel tetrazole inhibitors of MurB

(2018) Martina Hrast et al.   Chemical Biology & Drug Design

Machine learning in chemoinformatics and drug discovery

(2018) Yu-Chen Lo et al.   DRUG DISCOVERY TODAY

Revitalizing the drug pipeline: AntibioticDB, an open access database to aid antibacterial research and development

(2018) L J Farrell et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Predictive Model of Linear Antimicrobial Peptides Active against Gram-Negative Bacteria

(2018) Boris Vishnepolsky et al.   Journal of Chemical Information and Modeling

Prediction of the antimicrobial activity of walnut ( Juglans regia L. ) kernel aqueous extracts using artificial neural network and multiple linear regression

(2018) Hatice Kavuncuoglu et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Genome-wide mutant profiling predicts the mechanism of a Lipid II binding antibiotic

(2018) Marina Santiago et al.   Nature Chemical Biology

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

(2018) Gustavo Arango-Argoty et al.   Microbiome

Using Evolutionary Algorithms and Machine Learning to Explore Sequence Space for the Discovery of Antimicrobial Peptides

(2018) Mari Yoshida et al.   Chem

Survey of Machine Learning Techniques in Drug Discovery

(2018) Natalie Stephenson et al.   CURRENT DRUG METABOLISM

Computational chemistry in drug lead discovery and design

(2018) Claudio N. Cavasotto et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Advances with support vector machines for novel drug discovery

(2018) Vinicius Gonçalves Maltarollo et al.   Expert Opinion on Drug Discovery

Antibiotic discovery: History, methods and perspectives

(2018) Guillaume André Durand et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal Salmonella

(2018) Marcus Nguyen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data

(2018) Danesh Moradigaravand et al.   PLoS Computational Biology

Design, synthesis and antibacterial evaluation of novel pleuromutilin derivatives possessing piperazine linker

(2017) Mei-Ling Gao et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Is Multitask Deep Learning Practical for Pharma?

(2017) Bharath Ramsundar et al.   Journal of Chemical Information and Modeling

Incremental cost of nosocomial bacteremia according to the focus of infection and antibiotic sensitivity of the causative microorganism in a university hospital

(2017) Marta Riu et al.   MEDICINE

The Drug Repurposing Hub: a next-generation drug library and information resource

(2017) Steven M Corsello et al.   NATURE MEDICINE

Prediction of antibiotic resistance: time for a new preclinical paradigm?

(2017) Morten O. A. Sommer et al.   NATURE REVIEWS MICROBIOLOGY

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

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?

(2017) Ernest Y. Lee et al.   Interface Focus

Use of machine learning approaches for novel drug discovery

(2016) Angélica Nakagawa Lima et al.   Expert Opinion on Drug Discovery

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

How old are bacterial pathogens?

(2016) Mark Achtman   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

First Report of Ceftazidime-Avibactam Resistance in a KPC-3-Expressing Klebsiella pneumoniae Isolate

(2015) Romney M. Humphries et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Tales from the war on error: the art and science of curating QSAR data

(2015) Marvin Waldman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Deep learning

(2015) Yann LeCun et al.   NATURE

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

(2015) Michael K. Gilson et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

(2015) Phelim Bradley et al.   Nature Communications

PBP2a Mutations Causing High-Level Ceftaroline Resistance in Clinical Methicillin-Resistant Staphylococcus aureus Isolates

(2014) S. Wesley Long et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Machine-Learning Techniques Applied to Antibacterial Drug Discovery

(2014) Jacob D. Durrant et al.   Chemical Biology & Drug Design

Applying machine learning techniques for ADME-Tox prediction: a review

(2014) Vinícius Gonçalves Maltarollo et al.   Expert Opinion on Drug Metabolism & Toxicology

Discovering New Agents Active against Methicillin-Resistant Staphylococcus aureus with Ligand-Based Approaches

(2014) Ling Wang et al.   Journal of Chemical Information and Modeling

Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing

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

Bacterial Whole-Genome Sequencing Revisited: Portable, Scalable, and Standardized Analysis for Typing and Detection of Virulence and Antibiotic Resistance Genes

(2014) S. R. Leopold et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach

(2014) T. A. Kohl et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Molecular mechanisms of antibiotic resistance

(2014) Jessica M. A. Blair et al.   NATURE REVIEWS MICROBIOLOGY

Acquired Resistance of Mycobacterium tuberculosis to Bedaquiline

(2014) Koen Andries et al.   PLoS One

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types

(2013) Xuan Xiao et al.   ANALYTICAL BIOCHEMISTRY

Predicting Targeted Polypharmacology for Drug Repositioning and Multi- Target Drug Discovery

(2013) X. Liu et al.   CURRENT MEDICINAL CHEMISTRY

General Theory for Multiple Input-Output Perturbations in Complex Molecular Systems. 1. Linear QSPR Electronegativity Models in Physical, Organic, and Medicinal Chemistry

(2013) Humberto Gonzalez-Diaz et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Prospects for new antibiotics: a molecule-centered perspective

(2013) Christopher T Walsh et al.   JOURNAL OF ANTIBIOTICS

Whole-Genome Sequencing for Rapid Susceptibility Testing of M. tuberculosis

(2013) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

Inferring multi-target QSAR models with taxonomy-based multi-task learning

(2013) Lars Rosenbaum et al.   Journal of Cheminformatics

Challenges for Academic Drug Discovery

(2012) William L. Jorgensen   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Machine Learning Techniques and Drug Design

(2012) J.C. Gertrudes et al.   CURRENT MEDICINAL CHEMISTRY

Magic bullets and moving targets: antibiotic resistance and experimental chemotherapy, 1900-1940

(2012) Christoph Gradmann   Dynamis

Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification

(2012) P. J. Ballester et al.   Journal of the Royal Society Interface

Multi-Objective Optimization Methods in De Novo Drug Design

(2012) C. Nicolaou et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

Desirability-Based Multi-Objective QSAR in Drug Discovery

(2012) Maykel Cruz-Monteagudo et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

Comparative Susceptibilities to Fidaxomicin (OPT-80) of Isolates Collected at Baseline, Recurrence, and Failure from Patients in Two Phase III Trials of Fidaxomicin against Clostridium difficile Infection

(2011) Ellie J. C. Goldstein et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Jointly Handling Potency and Toxicity of Antimicrobial Peptidomimetics by Simple Rules from Desirability Theory and Chemoinformatics

(2011) Maykel Cruz-Monteagudo et al.   Journal of Chemical Information and Modeling

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

Structure-based drug design and modern medicine

(2010) R Vijayakrishnan   Journal of Postgraduate Medicine

A Brief History of the Antibiotic Era: Lessons Learned and Challenges for the Future

(2010) Rustam I. Aminov   Frontiers in Microbiology

Hospital and Societal Costs of Antimicrobial‐Resistant Infections in a Chicago Teaching Hospital: Implications for Antibiotic Stewardship

(2009) Rebecca R. Roberts et al.   CLINICAL INFECTIOUS DISEASES

AmpC  -Lactamases

(2009) G. A. Jacoby   CLINICAL MICROBIOLOGY REVIEWS

An Analysis of Ensemble Pruning Techniques Based on Ordered Aggregation

(2009) G. Martinez-Muoz et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Genetic Characterization of Vga ABC Proteins Conferring Reduced Susceptibility to Pleuromutilins in Staphylococcus aureus

(2008) D. R. Gentry et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bad Bugs, No Drugs: No ESKAPE! An Update from the Infectious Diseases Society of America

(2008) Helen W. Boucher et al.   CLINICAL INFECTIOUS DISEASES

80th Anniversary of the discovery of penicillin

(2008) Alasdair Geddes   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Desirability-based multiobjective optimization for global QSAR studies: Application to the design of novel NSAIDs with improved analgesic, antiinflammatory, and ulcerogenic profiles

(2008) Maykel Cruz-Monteagudo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY