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Predicting Binding Free Energies: Frontiers and Benchmarks

Annual review of biophysics, 2017-05, Vol.46 (1), p.531-558

2017

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Pathogenesis of Gram-Negative Bacteremia

Clinical microbiology reviews, 2021-06, Vol.34 (2)

2021

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Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

Annual review of biophysics, 2013-01, Vol.42 (1), p.121-142

2013

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Guidelines for the analysis of free energy calculations

Journal of computer-aided molecular design, 2015-05, Vol.29 (5), p.397-411

2015

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A systematic analysis of hypermucoviscosity and capsule reveals distinct and overlapping genes that impact Klebsiella pneumoniae fitness

PLoS pathogens, 2021-03, Vol.17 (3), p.e1009376-e1009376

2021

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Redundancy and Specificity of Escherichia coli Iron Acquisition Systems during Urinary Tract Infection

Infection and Immunity, 2011-03, Vol.79 (3), p.1225-1235

2011

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Perspective: Alchemical free energy calculations for drug discovery

The Journal of chemical physics, 2012-12, Vol.137 (23), p.230901-230901

2012

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Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

Nature chemistry, 2018-01, Vol.10 (1), p.8-16

2018

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Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Journal of the American Chemical Society, 2015-02, Vol.137 (7), p.2695-2703

2015

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Host-pathogen interactions in urinary tract infection

Nature reviews. Urology, 2010-08, Vol.7 (8), p.430-441

2010

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TnseqDiff: identification of conditionally essential genes in transposon sequencing studies

BMC bioinformatics, 2017-07, Vol.18 (1), p.326-11, Article 326

2017

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Complicated Catheter-Associated Urinary Tract Infections Due to Escherichia coli and Proteus mirabilis

Clinical Microbiology Reviews, 2008-01, Vol.21 (1), p.26-59

2008

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Initiation of Swarming Motility by Proteus mirabilis Occurs in Response to Specific Cues Present in Urine and Requires Excess l-Glutamine

Journal of Bacteriology, 2013-03, Vol.195 (6), p.1305-1319

2013

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Genome-wide transposon mutagenesis of Proteus mirabilis: Essential genes, fitness factors for catheter-associated urinary tract infection, and the impact of polymicrobial infection on fitness requirements

PLoS pathogens, 2017-06, Vol.13 (6), p.e1006434

2017

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Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water

Journal of chemical theory and computation, 2016-08, Vol.12 (8), p.4015-4024

2016

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Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects

The Journal of chemical physics, 2013-11, Vol.139 (18), p.184103-184103

2013

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Waging War against Uropathogenic Escherichia coli: Winning Back the Urinary Tract

Infection and Immunity, 2010-02, Vol.78 (2), p.568-585

2010

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Pathogenic Escherichia coli

Nature reviews. Microbiology, 2004-02, Vol.2 (2), p.123-140

2004

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MrpH, a new class of metal-binding adhesin, requires zinc to mediate biofilm formation

PLoS pathogens, 2020-08, Vol.16 (8), p.e1008707

2020

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The Klebsiella pneumoniae citrate synthase gene, gltA, influences site specific fitness during infection

PLoS pathogens, 2019-08, Vol.15 (8), p.e1008010-e1008010

2019

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A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations

Current topics in medicinal chemistry, 2017-01, Vol.17 (23), p.2577-2585

2017

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Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Journal of computer-aided molecular design, 2017-01, Vol.31 (1), p.147-161

2017

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Escherichia coli global gene expression in urine from women with urinary tract infection

PLoS pathogens, 2010-11, Vol.6 (11), p.e1001187-e1001187

2010

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An overview of the SAMPL8 host–guest binding challenge

Journal of computer-aided molecular design, 2022-10, Vol.36 (10), p.707-734

2022

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Immunization with the Yersiniabactin Receptor, FyuA, Protects against Pyelonephritis in a Murine Model of Urinary Tract Infection

Infection and Immunity, 2013-09, Vol.81 (9), p.3309-3316

2013

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Predicting Binding Free Energies: Frontiers and Benchmarks

Pathogenesis of Gram-Negative Bacteremia

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

Guidelines for the analysis of free energy calculations

A systematic analysis of hypermucoviscosity and capsule reveals distinct and overlapping genes that impact Klebsiella pneumoniae fitness

Redundancy and Specificity of Escherichia coli Iron Acquisition Systems during Urinary Tract Infection

Perspective: Alchemical free energy calculations for drug discovery

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Host-pathogen interactions in urinary tract infection

TnseqDiff: identification of conditionally essential genes in transposon sequencing studies

Complicated Catheter-Associated Urinary Tract Infections Due to Escherichia coli and Proteus mirabilis

Initiation of Swarming Motility by Proteus mirabilis Occurs in Response to Specific Cues Present in Urine and Requires Excess l-Glutamine

Genome-wide transposon mutagenesis of Proteus mirabilis: Essential genes, fitness factors for catheter-associated urinary tract infection, and the impact of polymicrobial infection on fitness requirements

Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects

Waging War against Uropathogenic Escherichia coli: Winning Back the Urinary Tract

Pathogenic Escherichia coli

MrpH, a new class of metal-binding adhesin, requires zinc to mediate biofilm formation

The Klebsiella pneumoniae citrate synthase gene, gltA, influences site specific fitness during infection

A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Escherichia coli global gene expression in urine from women with urinary tract infection

An overview of the SAMPL8 host–guest binding challenge

Immunization with the Yersiniabactin Receptor, FyuA, Protects against Pyelonephritis in a Murine Model of Urinary Tract Infection

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