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Machine learning differentiates enzymatic and non-enzymatic metals in proteins

Nature communications, 2021-06, Vol.12 (1), p.3712-3712, Article 3712

2021

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Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels

The journal of physical chemistry. B, 2021-04, Vol.125 (14), p.3622-3628

2021

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Correction to “Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels”

The journal of physical chemistry. B, 2021-10, Vol.125 (42), p.11784-11784

2021

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Control of Membrane Protein Topology by a Single C-Terminal Residue

Science (American Association for the Advancement of Science), 2010-06, Vol.328 (5986), p.1698-1700

2010

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Colicin E1 opens its hinge to plug TolC

eLife, 2022-02, Vol.11

2022

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Evolutionary Engineering a Larger Porin Using a Loop-to-Hairpin Mechanism

Journal of molecular biology, 2023-11, Vol.435 (22), p.168292-168292, Article 168292

2023

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High-Yield Preparation of Outer Membrane Protein Efflux Pumps by in Vitro Refolding is Concentration Dependent

The Journal of membrane biology, 2021-02, Vol.254 (1), p.41-50

2021

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Modulating Integrin αIIbβ3 Activity through Mutagenesis of Allosterically Regulated Intersubunit Contacts

Biochemistry (Easton), 2019-07, Vol.58 (30), p.3251-3259

2019

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Machine learning for enzyme engineering, selection and design

Protein engineering, design and selection, 2021-07, Vol.34

2021

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Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

PLoS computational biology, 2022-06, Vol.18 (6), p.e1010271-e1010271

2022

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Discovery and Characterization of Two Folded Intermediates for Outer Membrane Protein TolC Biogenesis

Journal of molecular biology, 2024-08, Vol.436 (16), p.168652, Article 168652

2024

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Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding

Journal of molecular biology, 2018-09, Vol.430 (18), p.3251-3265

2018

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General features of transmembrane beta barrels from a large database

Proceedings of the National Academy of Sciences - PNAS, 2023-07, Vol.120 (29), p.e2220762120-e2220762120

2023

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Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

eLife, 2018-11, Vol.7

2018

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Detergent headgroups control TolC folding in vitro

Biophysical journal, 2023-04, Vol.122 (7), p.1185-1197

2023

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MAHOMES II: A webserver for predicting if a metal binding site is enzymatic

Protein science, 2023-04, Vol.32 (4), p.e4626-n/a

2023

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KIF—Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes

The Journal of chemical physics, 2023-04, Vol.158 (14), p.144114-144114

2023

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Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction

PLoS computational biology, 2022-04, Vol.18 (4), p.e1009943-e1009943

2022

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Outer membrane protein evolution

Current opinion in structural biology, 2021-06, Vol.68, p.122-128

2021

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Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment

PLoS computational biology, 2023-11, Vol.19 (11), p.e1011621-e1011621

2023

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XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers

PLoS computational biology, 2021-09, Vol.17 (9), p.e1009037-e1009037

2021

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Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins

PLoS computational biology, 2024-03, Vol.20 (3), p.e1011939-e1011939

2024

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Membrane thinning and lateral gating are consistent features of BamA across multiple species

PLoS computational biology, 2020-10, Vol.16 (10), p.e1008355-e1008355

2020

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Outer membrane protein design

Current opinion in structural biology, 2017-08, Vol.45, p.45-52

Slusky, Joanna SG

2017

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Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold

Structure (London), 2018-09, Vol.26 (9), p.1266-1274.e2

2018

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Machine learning differentiates enzymatic and non-enzymatic metals in proteins

Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels

Correction to “Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels”

Control of Membrane Protein Topology by a Single C-Terminal Residue

Colicin E1 opens its hinge to plug TolC

Evolutionary Engineering a Larger Porin Using a Loop-to-Hairpin Mechanism

High-Yield Preparation of Outer Membrane Protein Efflux Pumps by in Vitro Refolding is Concentration Dependent

Modulating Integrin αIIbβ3 Activity through Mutagenesis of Allosterically Regulated Intersubunit Contacts

Machine learning for enzyme engineering, selection and design

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

Discovery and Characterization of Two Folded Intermediates for Outer Membrane Protein TolC Biogenesis

Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding

General features of transmembrane beta barrels from a large database

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

Detergent headgroups control TolC folding in vitro

MAHOMES II: A webserver for predicting if a metal binding site is enzymatic

KIF—Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes

Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction

Outer membrane protein evolution

Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment

XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers

Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins

Membrane thinning and lateral gating are consistent features of BamA across multiple species

Outer membrane protein design

Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold

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