List of works - Zaida Luthey-Schulten

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

scientific article published on 30 January 2007

Ab initio protein structure prediction.

scientific article

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

scientific article published on 25 March 2020

Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism

scientific article

Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations

scientific article

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

scientific article published on 01 November 2019

Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides

scientific article published in February 1999

Capture and quality control mechanisms for adenosine-5'-triphosphate binding

scientific article published on 13 February 2013

Careful accounting of extrinsic noise in protein expression reveals correlations among its sources

scientific article published on 27 June 2017

Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations

scientific article

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

scientific article published in October 2004

Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics

scientific article published on 23 October 2017

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

scientific article published on 06 February 2020

Computational Modeling of Fluctuations in Energy and Metabolic Pathways of Methanogenic Archaea

Correction: Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

scientific article published on 19 December 2017

Corrigendum: DNA looping increases the range of bistability in a stochastic model of the lac genetic switch (2013 Phys. Biol. 10 026002)

scholarly article published in Physical Biology

CryoEM-based hybrid modeling approaches for structure determination

scientific article published on 3 November 2017

Cytochrome c2Exit Strategy: Dissociation Studies and Evolutionary Implications

scientific article published on 01 January 2007

DNA looping increases the range of bistability in a stochastic model of the lac genetic switch.

scientific article published on 13 February 2013

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

scientific article published on 14 June 2011

Developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through HisF.

scientific article

Direction Matters: Monovalent Streptavidin/Biotin Complex under Load

scientific article published on 26 October 2018

Dynamical networks in tRNA:protein complexes

scholarly article

Dynamics of Recognition between tRNA and elongation factor Tu

scientific article published on 4 February 2008

Essential metabolism for a minimal cell

scientific article published on 18 January 2019

Estimation of Relative Protein-RNA Binding Strengths from Fluctuations in the Bound State

scientific article

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

scientific article published on May 2016

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

scientific article published on 8 September 2017

Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information.

scientific article

Evolutionary profiles from the QR factorization of multiple sequence alignments

scientific article

Exit strategies for charged tRNA from GluRS

scientific article published on 13 February 2010

Experimental and computational determination of tRNA dynamics

scientific article published on January 2010

Exploring residue component contributions to dynamical network models of allostery

scientific article

Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement

scientific article published on 17 June 2009

Extrinsic Noise Driven Phenotype Switching in a Self-Regulating Gene

scientific article published in Physical Review Letters

Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase

scientific article published on 17 April 2018

Functional role of ribosomal signatures

scientific article (publication date: 15 December 2010)

Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories

scientific article published on 01 October 2020

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function.

scientific article published on 04 January 2017

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

scientific article

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

scientific article published on August 2013

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

scientific article published on 29 July 2009

In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States

scientific article published on 02 July 2019

Influence of montmorillonite on nucleotide oligomerization reactions: a molecular dynamics study

scientific article published on 7 March 2010

Is the olfactory receptor a metalloprotein?

scientific article

Kinetic Modeling of the Genetic Information Processes in a Minimal Cell

scientific article published on 28 November 2019

Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation

scientific article

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

scientific article

Long time-scale simulations of in vivo diffusion using GPU hardware

article published in 2009

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

scientific article published on 09 September 2019

Molecular dynamics simulations of substrate channeling through an α–β barrel protein

article

Molecular signatures of ribosomal evolution

scientific article (publication date: 16 September 2008)

MultiSeq: unifying sequence and structure data for evolutionary analysis

scientific article published on 16 August 2006

Multiple Alignment of protein structures and sequences for VMD.

scientific article

NAMD goes quantum: an integrative suite for hybrid simulations

scientific article published on 26 March 2018

Native conformational dynamics of the spliceosomal U1A protein

scientific article published on 24 February 2015

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

scientific article published on May 23, 2011

NetworkView: 3D display and analysis of protein·RNA interaction networks

scientific article published on 14 September 2012

Noise contributions in an inducible genetic switch: a whole-cell simulation study

scientific article

On the evolution of structure in aminoacyl-tRNA synthetases

scientific article

On the physical basis of the amino acid polar requirement.

scientific article published on 29 April 2008

On the structure of hisH: protein structure prediction in the context of structural and functional genomics.

scientific article

Optimizing physical energy functions for protein folding

scientific article published in January 2004

Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

scientific article

Population FBA predicts metabolic phenotypes in yeast.

scientific article published on 8 September 2017

Protein-guided RNA dynamics during early ribosome assembly.

scientific article published on 12 February 2014

Ribosome biogenesis in replicating cells: Integration of experiment and theory

scientific article published on 13 June 2016

Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape

scientific article published on 14 August 2017

Role of Water in Transient Cytochrome c2Docking

Scalable molecular dynamics on CPU and GPU architectures with NAMD ⬇️

scientific article published on 01 July 2020

Self-consistently optimized energy functions for protein structure prediction by molecular dynamics

scientific article

Simulating Biological Processes: Stochastic Physics from Whole Cells to Colonies.

scientific article published on 9 February 2018

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations.

scientific article

Spatially-resolved metabolic cooperativity within dense bacterial colonies

scientific article

Statistical mechanical refinement of protein structure prediction schemes. II. Mayer cluster expansion approach

Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach

Stochastic Simulations of Cellular Processes: From Single Cells to Colonies

Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus.

scientific article published in May 1997

Structural elements in IGP synthase exclude water to optimize ammonia transfer.

scientific article

Structural intermediates and folding events in the early assembly of the ribosomal small subunit

scientific article

Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations

scientific article published on 10 January 2020

The Conformational Change in Elongation Factor Tu Involves Separation of Its Domains

scientific article

The evolutionary history of Cys-tRNACys formation

scientific article

The foldon universe: a survey of structural similarity and self-recognition of independently folding units 1 1Edited by F. E. Cohen

The role of L1 stalk-tRNA interaction in the ribosome elongation cycle

scientific article

Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome <i>bc</i><sub>1</sub> Complex

scientific article published on 05 January 2021

Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly

scientific article

Towards a computational model of a methane producing archaeum

scientific article (publication date: 2014)

Variations in the fast folding rates of the lambda-repressor: a hybrid molecular dynamics study

scientific article

Visualizing the dual space of biological molecules.

scientific article

Water in protein structure prediction

scientific article

Whole Cell Modeling: From Single Cells to Colonies

scientific article published on 31 July 2014

List of works by Zaida Luthey-Schulten

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

Ab initio protein structure prediction.

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism

Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides

Capture and quality control mechanisms for adenosine-5'-triphosphate binding

Careful accounting of extrinsic noise in protein expression reveals correlations among its sources

Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations

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

Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics

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

Computational Modeling of Fluctuations in Energy and Metabolic Pathways of Methanogenic Archaea

Correction: Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

Corrigendum: DNA looping increases the range of bistability in a stochastic model of the lac genetic switch (2013 Phys. Biol. 10 026002)

CryoEM-based hybrid modeling approaches for structure determination

Cytochrome c2Exit Strategy: Dissociation Studies and Evolutionary Implications

DNA looping increases the range of bistability in a stochastic model of the lac genetic switch.

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

Developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through HisF.

Direction Matters: Monovalent Streptavidin/Biotin Complex under Load

Dynamical networks in tRNA:protein complexes

Dynamics of Recognition between tRNA and elongation factor Tu

Essential metabolism for a minimal cell

Estimation of Relative Protein-RNA Binding Strengths from Fluctuations in the Bound State

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

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

Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information.

Evolutionary profiles from the QR factorization of multiple sequence alignments

Exit strategies for charged tRNA from GluRS

Experimental and computational determination of tRNA dynamics

Exploring residue component contributions to dynamical network models of allostery

Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement

Extrinsic Noise Driven Phenotype Switching in a Self-Regulating Gene

Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase

Functional role of ribosomal signatures

Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function.

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

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

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

In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States

Influence of montmorillonite on nucleotide oligomerization reactions: a molecular dynamics study

Is the olfactory receptor a metalloprotein?

Kinetic Modeling of the Genetic Information Processes in a Minimal Cell

Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation

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

Long time-scale simulations of in vivo diffusion using GPU hardware

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

Molecular dynamics simulations of substrate channeling through an α–β barrel protein

Molecular signatures of ribosomal evolution

MultiSeq: unifying sequence and structure data for evolutionary analysis

Multiple Alignment of protein structures and sequences for VMD.

NAMD goes quantum: an integrative suite for hybrid simulations

Native conformational dynamics of the spliceosomal U1A protein

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

NetworkView: 3D display and analysis of protein·RNA interaction networks

Noise contributions in an inducible genetic switch: a whole-cell simulation study

On the evolution of structure in aminoacyl-tRNA synthetases

On the physical basis of the amino acid polar requirement.

On the structure of hisH: protein structure prediction in the context of structural and functional genomics.

Optimizing physical energy functions for protein folding

Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

Population FBA predicts metabolic phenotypes in yeast.

Protein-guided RNA dynamics during early ribosome assembly.

Ribosome biogenesis in replicating cells: Integration of experiment and theory

Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape

Role of Water in Transient Cytochrome c2Docking

Scalable molecular dynamics on CPU and GPU architectures with NAMD ⬇️

Self-consistently optimized energy functions for protein structure prediction by molecular dynamics

Simulating Biological Processes: Stochastic Physics from Whole Cells to Colonies.

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations.

Spatially-resolved metabolic cooperativity within dense bacterial colonies

Statistical mechanical refinement of protein structure prediction schemes. II. Mayer cluster expansion approach

Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach

Stochastic Simulations of Cellular Processes: From Single Cells to Colonies

Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus.

Structural elements in IGP synthase exclude water to optimize ammonia transfer.