Zaida Luthey-Schulten
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American chemist
Zaida Luthey-Schulten's AcademicInfluence.com Rankings
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Chemistry
Zaida Luthey-Schulten's Degrees
- PhD Chemistry University of California, San Diego
- Bachelors Chemistry University of California, San Diego
Why Is Zaida Luthey-Schulten Influential?
(Suggest an Edit or Addition)According to Wikipedia, Zaida Ann "Zan" Luthey-Schulten is the William and Janet Lycan Professor of Chemistry at the University of Illinois at Urbana-Champaign. She was promoted to professor in 2004. She is also involved with the NASA Astrobiology Institute.
Zaida Luthey-Schulten's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Scalable molecular dynamics on CPU and GPU architectures with NAMD. (2020) (929)
- Dynamical networks in tRNA:protein complexes (2009) (610)
- Toward an outline of the topography of a realistic protein-folding funnel. (1995) (453)
- MultiSeq: unifying sequence and structure data for evolutionary analysis (2006) (369)
- Ab initio protein structure prediction. (2002) (307)
- Optimal protein-folding codes from spin-glass theory. (1992) (300)
- Protein folding funnels: the nature of the transition state ensemble. (1996) (295)
- Water in protein structure prediction. (2004) (270)
- On the Evolution of Structure in Aminoacyl-tRNA Synthetases (2003) (234)
- Protein tertiary structure recognition using optimized Hamiltonians with local interactions. (1992) (204)
- Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer (1999) (180)
- Classical force field parameters for the heme prosthetic group of cytochrome c (2004) (172)
- Foldons, protein structural modules, and exons. (1996) (161)
- NetworkView: 3D display and analysis of protein·RNA interaction networks (2012) (159)
- Exploring residue component contributions to dynamical network models of allostery. (2012) (146)
- Protein-guided RNA dynamics during early ribosome assembly (2014) (134)
- Is the olfactory receptor a metalloprotein? (2003) (125)
- Multiple Alignment of protein structures and sequences for VMD (2006) (125)
- Determining the stability of genetic switches: explicitly accounting for mRNA noise. (2011) (114)
- Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites (2011) (112)
- Molecular signatures of ribosomal evolution (2008) (110)
- Lattice microbes: High‐performance stochastic simulation method for the reaction‐diffusion master equation (2013) (108)
- The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. (2010) (104)
- Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study (2011) (104)
- Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population (2013) (103)
- NAMD goes quantum: An integrative suite for QM/MM simulations (2018) (99)
- Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus (1997) (98)
- Optimizing physical energy functions for protein folding (2003) (87)
- A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase. (2007) (83)
- Evaluating protein structure-prediction schemes using energy landscape theory (2001) (79)
- The evolutionary history of Cys-tRNACys formation. (2005) (77)
- Gas‐phase methanol solvation of Cs+ : Vibrational spectroscopy and Monte Carlo simulation (1990) (73)
- The foldon universe: a survey of structural similarity and self-recognition of independently folding units. (1997) (73)
- Essential metabolism for a minimal cell (2019) (72)
- Dynamics of Recognition between tRNA and elongation factor Tu. (2008) (72)
- Self-consistently optimized energy functions for protein structure prediction by molecular dynamics. (1998) (70)
- Self‐consistently optimized statistical mechanical energy functions for sequence structure alignment (1996) (67)
- Spatially-resolved metabolic cooperativity within dense bacterial colonies (2015) (67)
- Experimental and computational determination of tRNA dynamics (2010) (64)
- Extrinsic noise driven phenotype switching in a self-regulating gene. (2013) (63)
- Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides (1999) (57)
- Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase. (2005) (52)
- Helix-Coil, Liquid Crystal, and Spin Glass Transitions of a Collapsed Heteropolymer (1995) (52)
- Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information. (2005) (52)
- Long time-scale simulations of in vivo diffusion using GPU hardware (2009) (51)
- Folding funnels: The key to robust protein structure prediction (2002) (48)
- Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy (2019) (47)
- Developing an energy landscape for the novel function of a (β/α)8 barrel: Ammonia conduction through HisF (2003) (46)
- Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics. (2017) (45)
- Evolutionary profiles from the QR factorization of multiple sequence alignments. (2005) (44)
- Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach (2002) (43)
- On the Physical Basis of the Amino Acid Polar Requirement (2008) (41)
- Molecular dynamics simulations of substrate channeling through an α–β barrel protein (2004) (40)
- Structural elements in IGP synthase exclude water to optimize ammonia transfer. (2005) (40)
- Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations (2014) (39)
- Direction Matters: Monovalent Streptavidin/Biotin Complex under Load. (2018) (38)
- Three-dimensional model for the hormone binding domains of steroid receptors. (1993) (37)
- DNA looping increases the range of bistability in a stochastic model of the lac genetic switch (2013) (37)
- Effects of DNA replication on mRNA noise (2015) (35)
- Exit strategies for charged tRNA from GluRS. (2010) (35)
- Fundamental behaviors emerge from simulations of a living minimal cell (2022) (35)
- Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories. (2020) (34)
- Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain (2020) (33)
- From Sequence to Structure (2003) (31)
- Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. (2007) (31)
- Variations in the fast folding rates of the λ-repressor: A hybrid molecular dynamics study (2004) (30)
- Role of water in transient cytochrome c2 docking (2004) (29)
- Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations (2020) (29)
- Simulating biological processes: stochastic physics from whole cells to colonies (2018) (28)
- In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States (2019) (28)
- Barriers to Forced Transitions in Polysaccharides (2000) (26)
- Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes (2017) (26)
- Influence of Montmorillonite on Nucleotide Oligomerization Reactions: A Molecular Dynamics Study (2010) (25)
- Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4 (2009) (25)
- Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly. (2015) (24)
- Cytochrome c2 Exit Strategy: Dissociation Studies and Evolutionary Implications (2007) (24)
- Functional role of ribosomal signatures. (2010) (21)
- Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations. (2012) (21)
- Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans (2016) (21)
- CryoEM-based hybrid modeling approaches for structure determination. (2018) (21)
- Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads (2016) (20)
- Population FBA predicts metabolic phenotypes in yeast (2017) (19)
- Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function (2017) (19)
- Careful accounting of extrinsic noise in protein expression reveals correlations among its sources. (2017) (17)
- Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism. (2015) (17)
- Membrane organisation of photosystem I complexes in the most abundant phototroph on Earth (2019) (17)
- Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape. (2017) (16)
- Towards a Computational Model of a Methane Producing Archaeum (2014) (15)
- Leucyl-tRNA synthetase editing domain functions as a molecular rheostat to control codon ambiguity in Mycoplasma pathogens (2013) (15)
- On the structure of hisH: protein structure prediction in the context of structural and functional genomics. (2001) (15)
- Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories (2020) (14)
- An in-silico human cell model reveals the influence of spatial organization on RNA splicing (2020) (14)
- Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations. (2017) (14)
- Developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through HisF. (2003) (13)
- THE STATISTICAL MECHANICAL BASIS OF SEQUENCE ALIGNMENT ALGORITHMS FOR PROTEIN STRUCTURE RECOGNITION (1996) (12)
- Statistical mechanical refinement of protein structure prediction schemes. II. Mayer cluster expansion approach (2003) (12)
- Native conformational dynamics of the spliceosomal U1A protein. (2015) (11)
- Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase (2018) (11)
- Water in protein structure prediction - eScholarship (2004) (11)
- Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales (2020) (11)
- The Conformational Change in Elongation Factor Tu Involves Separation of Its Domains. (2017) (10)
- Ribosome biogenesis in replicating cells: Integration of experiment and theory (2016) (10)
- Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects (2017) (10)
- Cytochrome c(2) Exit Strategy: Dissociation Studies and Evolutionary Implications. (2007) (10)
- A Bayesian approach to sequence alignment algorithms for protein structure recognition (1994) (9)
- Structural intermediates and folding events in the early assembly of the ribosomal small subunit. (2013) (9)
- Integrating experiments, theory and simulations into whole-cell models (2021) (9)
- A Problem Solving Environment for Stochastic Biological Simulations (2013) (9)
- Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps (2021) (8)
- Kinetic Modeling of the Genetic Information Processes in a Minimal Cell (2019) (8)
- Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome bc1 Complex. (2021) (8)
- Variations in the fast folding rates of the lambda-repressor: a hybrid molecular dynamics study. (2004) (7)
- Bacteria on steroids: the enzymatic mechanism of an NADH-dependent dehydrogenase that regulates the conversion of cortisol to androgen in the gut microbiome (2020) (7)
- Whole Cell Modeling: From Single Cells to Colonies. (2014) (7)
- Corrigendum: DNA looping increases the range of bistability in a stochastic model of the lac genetic switch (2013 Phys. Biol. 10 026002) (2014) (7)
- Stochastic Simulations of Cellular Processes: From Single Cells to Colonies (2014) (7)
- Capture and quality control mechanisms for adenosine-5'-triphosphate binding. (2013) (6)
- Improving Reaction Kernel Performance in Lattice Microbes: Particle-Wise Propensities and Run-Time Generated Code (2016) (6)
- Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA (2021) (6)
- Metabolite Damage and Damage Control in a Minimal Genome (2021) (6)
- Hybrid CME–ODE method for efficient simulation of the galactose switch in yeast (2018) (5)
- Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase (2021) (5)
- Bioinformatics and Sequence Alignment (2005) (5)
- Extrinsic Noise Driven Phenotype Switching in a Self-Regulating Gene (2014) (5)
- Estimation of Relative Protein-RNA Binding Strengths from Fluctuations in the Bound State. (2016) (4)
- Simulating Dynamics in RNA–Protein Complexes (2012) (4)
- Foldons as independently folding units of proteins (1997) (3)
- Molecular dynamics simulation of an entire cell (2023) (3)
- Integrating cellular and molecular structures and dynamics into whole-cell models. (2022) (3)
- Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) (3)
- Protein tertiary structure recognition using optimized associative memory Hamiltonians (1993) (3)
- Stochastic Analysis Demonstrates the Dual Role of Hfq in Chaperoning E. coli Sugar Shock Response (2020) (2)
- Complete structure of the core signalling unit of the E. coli chemosensory array in an optimised minicell strain (2019) (2)
- Direct Measurement of Stepping Dynamics of E. coli UvrD Helicase (2020) (1)
- Electrostatic Interaction Effects on the Binding of Spliceosomal U1A Protein-SL2 RNA Hairpin (2015) (1)
- An In-Silico Mammalian Whole-Cell Model Reveals the Influence of Spatial Organization on RNA Splicing Efficiency (2018) (1)
- Visualizing the dual space of biological molecules (2006) (1)
- Erratum: Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population (Proceedings of the National Academy of Sciences of the United States of America (2013) 110(14006-14011) DOI:10.1073/pnas.1222569110) (2014) (1)
- Heterogenity in Protein Copy Numbers induces Metabolic Variability in Modeled E. coli Populations (2013) (1)
- Single Molecule Views of the Ribosome Assembly (2012) (0)
- Determining Force Fields (2003) (0)
- Hierarchical Folding of the rRNA in the Early Assembly of the E. Coli Ribosomal Small Subunit (2014) (0)
- Stochastic Simulations of Cellular Processes in Bacteria (2013) (0)
- Integration of Reaction-Diffusion Master Equation and Brownian Dynamics Methodologies to Simulate a Minimal Cell (2019) (0)
- Supporting Information for “ Evolutionary profiles from the QR factorization of multiple sequence alignments ” (2005) (0)
- Modeling Metabolic Variability in Methanosarcina Acetivorans (2014) (0)
- Molecular Mechanism of Conformational Switching that Regulates Helicase Function (2020) (0)
- Chapter 13 – Stochastic Simulations of Cellular Processes: From Single Cells to Colonies (2014) (0)
- Crystal structure of the LeuRS editing domain of Candida albicans in complex with the adduct AN2690-AMP (2015) (0)
- Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes (2017) (0)
- New QMMM Interface to NAMD Probes tRNA Charging Mechanism (2018) (0)
- Foldons , protein structural modules , and exons ( protein folding / folding domains / structural domains ) (2005) (0)
- Determining the stability of genetic switches: beyond protein-only models (2011) (0)
- Deciphering the influence of genome architecture in minimized bacteria. (2023) (0)
- Dynamical Network Analysis of Protein:RNA Complexes Made Easy (2019) (0)
- WKB approach for determining the epigenetic stability of gene expression switches (2011) (0)
- Modeling the Impact of Point Mutations on the Regulatory Potency of the Small RNA SgrS (2019) (0)
- 4D dynamical whole-cell simulations of a growing minimal cell. (2023) (0)
- Fundamental cell behavior emerges from whole cell simulations of a minimal cell by integrating experiment and theory (2022) (0)
- Author response: Essential metabolism for a minimal cell (2018) (0)
- Correction: Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects (2017) (0)
- Modeling the Lipid Metabolism of a Genetically Minimal Cell (2020) (0)
- Modelling the Genetic Information Processes of a Genetically Minimal Cell (2020) (0)
- Modelling the Nucleotide Metabolic Network of a Genetically Minimal Cell (2020) (0)
- The effect of extrinsic noise on cellular decision making (2013) (0)
- Role of horizontal gene transfer as a control on the coevolution of ribosomal proteins and the genetic code (2011) (0)
- Progress report for Department of Energy grant The role of horizontal gene transfer as a control on the coevolution of ribosomal proteins and the genetic code (2011) (0)
- Elucidating Metabolic Variability in Isogenic Microbial Populations Arising due to Noise in Protein Expression (2014) (0)
- Artificial Neural Network based String Matching Algorithms for Species Classification – A Preliminary Study and Experimental Results (2016) (0)
- Spatial Organization of Ribosome Biogenesis of Escherichia Coli (2015) (0)
- The addition of a coarse-grained looping state enhances bistability in a gene expression model of lac (2013) (0)
- Stochastic Spatial Simulation of Genetic Information Processes in the Minimal Cell (2021) (0)
- Whole-Cell Simulations of mRNA Production in Eukaryotic Cell Models (2017) (0)
- Translation in the RNA World: Insight from the Proto-Ribosome Model (2013) (0)
- Unveiling the Rate-Limiting Step of the Bc1 Complex Reaction Mechanism (2019) (0)
- Towards Simulating Bacterial and Eukaryotic Cells: Integration of Experiment and Theory (2019) (0)
- Supporting Information for “ The evolutionary history of Cys-tRNA Cys formation ” (2005) (0)
- Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans (2016) (0)
- The onset of whole-cell modeling using the martini force field. (2023) (0)
- Author response: Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase (2018) (0)
- Effects of individual base-pairs on in vivo target search and destruction kinetics of small RNA (2020) (0)
- A Computational Human Whole-Cell Model Reveals the Effects of Spatial Organization on RNA Splicing (2019) (0)
- Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site (2013) (0)
- Toward a Spatially-Resolved Model of Metabolism in Dense Bacterial Colonies (2014) (0)
- Crystal structure of the LeuRS editing domain of Candida albicans Mutant K510A (2015) (0)
- Coarse-Grained Simulations of Nucleoid Structure (2014) (0)
- Crystal structure of the LeuRS editing domain of Candida albicans Mutant K510A in complex with the adduct formed by AN2690-AMP (2015) (0)
- Generating Chromosome Geometries at the Single-Cell Level from Cryo-Electron Tomograms (2021) (0)
- A Study of Global Motions in the Folding of Small Proteins (2001) (0)
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