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Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation

Journal of computational chemistry, 2013-01, Vol.34 (3), p.245-255

2013

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MultiSeq: unifying sequence and structure data for evolutionary analysis

BMC bioinformatics, 2006-08, Vol.7 (1), p.382-382, Article 382

2006

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Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain

Nature communications, 2020-02, Vol.11 (1), p.743-743, Article 743

2020

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Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase

Nature communications, 2021-12, Vol.12 (1), p.7015-14, Article 7015

2021

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Integrating experiments, theory and simulations into whole-cell models

Nature methods, 2021-05, Vol.18 (5), p.446-447

Luthey-Schulten, Zaida

2021

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Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population

Proceedings of the National Academy of Sciences - PNAS, 2013-08, Vol.110 (34), p.14006-14011

2013

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Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA

Nature communications, 2021-02, Vol.12 (1), p.874-874, Article 874

2021

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Effects of DNA replication on mRNA noise

Proceedings of the National Academy of Sciences - PNAS, 2015-12, Vol.112 (52), p.15886-15891

2015

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Classical force field parameters for the heme prosthetic group of cytochrome c

Journal of computational chemistry, 2004-10, Vol.25 (13), p.1613-1622

2004

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Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites

Proceedings of the National Academy of Sciences - PNAS, 2011-06, Vol.108 (23), p.9378-9383

2011

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Dynamical networks in tRNA:protein complexes

Proceedings of the National Academy of Sciences - PNAS, 2009-04, Vol.106 (16), p.6620-6625

2009

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Determining the stability of genetic switches: explicitly accounting for mRNA noise

Physical review letters, 2011-06, Vol.106 (24), p.248102-248102, Article 248102

2011

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Optimizing physical energy functions for protein folding

Proteins, structure, function, and bioinformatics, 2004-01, Vol.54 (1), p.88-103

2004

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Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy

Journal of the American Chemical Society, 2019-09, Vol.141 (37), p.14752-14763

2019

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Direction Matters: Monovalent Streptavidin/Biotin Complex under Load

Nano letters, 2019-06, Vol.19 (6), p.3415-3421

2019

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Spatially-resolved metabolic cooperativity within dense bacterial colonies

BMC systems biology, 2015-03, Vol.9 (1), p.15-15, Article 15

2015

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On the Evolution of Structure in Aminoacyl-tRNA Synthetases

Microbiology and Molecular Biology Reviews, 2003-12, Vol.67 (4), p.550-573

2003

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Simulating biological processes: stochastic physics from whole cells to colonies

Reports on progress in physics, 2018-05, Vol.81 (5), p.52601-052601

2018

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Is the Olfactory Receptor a Metalloprotein?

Proceedings of the National Academy of Sciences - PNAS, 2003-03, Vol.100 (6), p.3035-3039

2003

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A Network of Conserved Interactions Regulates the Allosteric Signal in a Glutamine Amidotransferase

Biochemistry (Easton), 2007-02, Vol.46 (8), p.2156-2173

2007

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Leucyl-tRNA synthetase editing domain functions as a molecular rheostat to control codon ambiguity in Mycoplasma pathogens

Proceedings of the National Academy of Sciences - PNAS, 2013-03, Vol.110 (10), p.3817-3822

2013

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Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4

BMC evolutionary biology, 2009-07, Vol.9 (1), p.179, Article 179

2009

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Molecular dynamics simulation of an entire cell

Frontiers in chemistry, 2023-01, Vol.11, p.1106495

2023

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Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes

Nature communications, 2017-09, Vol.8 (1), p.492-9, Article 492

2017

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The Role of L1 Stalk–tRNA Interaction in the Ribosome Elongation Cycle

Journal of molecular biology, 2010-10, Vol.402 (4), p.741-760

2010

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Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation

MultiSeq: unifying sequence and structure data for evolutionary analysis

Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain

Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase

Integrating experiments, theory and simulations into whole-cell models

Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population

Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA

Effects of DNA replication on mRNA noise

Classical force field parameters for the heme prosthetic group of cytochrome c

Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites

Dynamical networks in tRNA:protein complexes

Determining the stability of genetic switches: explicitly accounting for mRNA noise

Optimizing physical energy functions for protein folding

Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy

Direction Matters: Monovalent Streptavidin/Biotin Complex under Load

Spatially-resolved metabolic cooperativity within dense bacterial colonies

On the Evolution of Structure in Aminoacyl-tRNA Synthetases

Simulating biological processes: stochastic physics from whole cells to colonies

Is the Olfactory Receptor a Metalloprotein?

A Network of Conserved Interactions Regulates the Allosteric Signal in a Glutamine Amidotransferase

Leucyl-tRNA synthetase editing domain functions as a molecular rheostat to control codon ambiguity in Mycoplasma pathogens

Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4

Molecular dynamics simulation of an entire cell

Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes

The Role of L1 Stalk–tRNA Interaction in the Ribosome Elongation Cycle

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