Zaida A. Luthey-Schulten - Publications

Affiliations: 
Chemistry University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Area:
Prediction of Protein Structure and Function
Website:
http://www.chemistry.illinois.edu/faculty/Zaida_Luthey_Schulten.html

118 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Barragan AM, Soudackov AV, Luthey-Schulten Z, Hammes-Schiffer S, Schulten K, Solov'yov IA. Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome Complex. Journal of the American Chemical Society. PMID 33397104 DOI: 10.1021/jacs.0c07799  0.419
2020 Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, Buch R, Fiorin G, Hénin J, Jiang W, McGreevy R, Melo MCR, Radak BK, Skeel RD, Singharoy A, ... ... Luthey-Schulten Z, et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153: 044130. PMID 32752662 DOI: 10.1063/5.0014475  0.614
2020 Ghaemi Z, Peterson JR, Gruebele M, Luthey-Schulten Z. An in-silico human cell model reveals the influence of spatial organization on RNA splicing. Plos Computational Biology. 16: e1007717. PMID 32210422 DOI: 10.1371/Journal.Pcbi.1007717  0.312
2020 Burt A, Cassidy CK, Ames P, Bacia-Verloop M, Baulard M, Huard K, Luthey-Schulten Z, Desfosses A, Stansfeld PJ, Margolin W, Parkinson JS, Gutsche I. Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain. Nature Communications. 11: 743. PMID 32029744 DOI: 10.1038/S41467-020-14350-9  0.308
2019 Thornburg ZR, Melo MCR, Bianchi D, Brier TA, Crotty C, Breuer M, Smith HO, Hutchison CA, Glass JI, Luthey-Schulten Z. Kinetic Modeling of the Genetic Information Processes in a Minimal Cell. Frontiers in Molecular Biosciences. 6: 130. PMID 31850364 DOI: 10.3389/Fmolb.2019.00130  0.316
2019 Singharoy A, Maffeo C, Delgado-Magnero KH, Swainsbury DJK, Sener M, Kleinekathöfer U, Vant JW, Nguyen J, Hitchcock A, Isralewitz B, Teo I, Chandler DE, Stone JE, Phillips JC, Pogorelov TV, ... ... Luthey-Schulten Z, et al. Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell. 179: 1098-1111.e23. PMID 31730852 DOI: 10.1016/J.Cell.2019.10.021  0.768
2019 Bernardi RC, Durner E, Schoeler C, Malinowska KH, Carvalho BG, Bayer EA, Luthey-Schulten Z, Gaub HE, Nash MA. Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy. Journal of the American Chemical Society. PMID 31464132 DOI: 10.1021/Jacs.9B06776  0.399
2019 Yang W, Cassidy CK, Ames P, Diebolder CA, Schulten K, Luthey-Schulten Z, Parkinson JS, Briegel A. Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States. Mbio. 10. PMID 31266867 DOI: 10.1128/Mbio.00973-19  0.491
2019 Breuer M, Earnest TM, Merryman C, Wise KS, Sun L, Lynott MR, Hutchison CA, Smith HO, Lapek JD, Gonzalez DJ, de Crécy-Lagard V, Haas D, Hanson AD, Labhsetwar P, Glass JI, ... Luthey-Schulten Z, et al. Essential metabolism for a minimal cell. Elife. 8. PMID 30657448 DOI: 10.7554/Elife.36842  0.304
2019 dos Reis Melo MC, Bernardi RC, Luthey-Schulten Z. Dynamical Network Analysis of Protein:RNA Complexes Made Easy Biophysical Journal. 116: 562a-563a. DOI: 10.1016/J.Bpj.2018.11.3025  0.344
2019 Barragan AM, Soudackov AV, Luthey-Schulten Z, Schulten K, Hammes-Schiffer S, Solov'yov I. Unveiling the Rate-Limiting Step of the Bc1 Complex Reaction Mechanism Biophysical Journal. 116: 419a. DOI: 10.1016/J.Bpj.2018.11.2257  0.414
2018 Ma W, Whitley KD, Chemla YR, Luthey-Schulten Z, Schulten K. Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase. Elife. 7. PMID 29664402 DOI: 10.7554/Elife.34186  0.528
2018 Melo MCR, Bernardi RC, Rudack T, Scheurer M, Riplinger C, Phillips JC, Maia JDC, Rocha GB, Ribeiro JV, Stone JE, Neese F, Schulten K, Luthey-Schulten Z. NAMD goes quantum: an integrative suite for hybrid simulations. Nature Methods. PMID 29578535 DOI: 10.1038/Nmeth.4638  0.46
2018 Earnest T, Cole JA, Luthey-Schulten Z. Simulating Biological Processes: Stochastic Physics from Whole Cells to Colonies. Reports On Progress in Physics. Physical Society (Great Britain). PMID 29424367 DOI: 10.1088/1361-6633/Aaae2C  0.336
2018 Ma W, Whitley KD, Chemla YR, Luthey-Schulten Z, Schulten K. Author response: Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase Elife. DOI: 10.7554/Elife.34186.031  0.461
2018 Bianchi DM, Peterson JR, Earnest TM, Hallock MJ, Luthey-Schulten Z. Hybrid CME–ODE method for efficient simulation of the galactose switch in yeast Iet Systems Biology. 12: 170-176. DOI: 10.1049/Iet-Syb.2017.0070  0.315
2018 Melo MC, Bernardi RC, Schulten K, Luthey-Schulten Z. New QMMM Interface to NAMD Probes tRNA Charging Mechanism Biophysical Journal. 114: 674a-675a. DOI: 10.1016/J.Bpj.2017.11.3637  0.435
2017 Cassidy CK, Himes BA, Luthey-Schulten Z, Zhang P. CryoEM-based hybrid modeling approaches for structure determination. Current Opinion in Microbiology. 43: 14-23. PMID 29107896 DOI: 10.1016/J.Mib.2017.10.002  0.308
2017 Verdorfer T, Bernardi R, Meinhold A, Ott W, Luthey-Schulten Z, Nash MA, Gaub HE. Combining in Vitro and in Silico Single Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics. Journal of the American Chemical Society. PMID 29058444 DOI: 10.1021/Jacs.7B07574  0.338
2017 Lai J, Ghaemi Z, Luthey-Schulten Z. Conformational change in Elongation factor-Tu involves separation of its domains. Biochemistry. PMID 29045140 DOI: 10.1021/Acs.Biochem.7B00591  0.344
2017 Abeysirigunawardena SC, Kim H, Lai J, Ragunathan K, Rappé MC, Luthey-Schulten Z, Ha T, Woodson SA. Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes. Nature Communications. 8: 492. PMID 28887451 DOI: 10.1038/S41467-017-00536-1  0.429
2017 Labhsetwar P, Melo MCR, Cole JA, Luthey-Schulten Z. Population FBA predicts metabolic phenotypes in yeast. Plos Computational Biology. 13: e1005728. PMID 28886026 DOI: 10.1371/Journal.Pcbi.1005728  0.317
2017 Ghaemi Z, Guzman I, Gnutt D, Luthey-Schulten Z, Gruebele M. Role of Electrostatics in Protein-RNA Binding: The Global vs. the Local Energy Landscape. The Journal of Physical Chemistry. B. PMID 28806086 DOI: 10.1021/Acs.Jpcb.7B04318  0.365
2017 Cole JA, Luthey-Schulten Z. Careful accounting of extrinsic noise in protein expression reveals correlations among its sources. Physical Review. E. 95: 062418. PMID 28709241 DOI: 10.1103/Physreve.95.062418  0.302
2017 Earnest TM, Watanabe R, Stone JE, Mahamid J, Baumeister W, Villa E, Luthey-Schulten Z. Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations. The Journal of Physical Chemistry. B. PMID 28291359 DOI: 10.1021/Acs.Jpcb.7B00672  0.355
2016 Ghaemi Z, Guzman I, Baek JJ, Gruebele M, Luthey-Schulten Z. Estimation of Relative Protein-RNA Binding Strengths from Fluctuations in the Bound State. Journal of Chemical Theory and Computation. PMID 27529183 DOI: 10.1021/Acs.Jctc.6B00418  0.362
2016 Stone JE, Hallock MJ, Phillips JC, Peterson JR, Luthey-Schulten Z, Schulten K. Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads. Ieee International Symposium On Parallel & Distributed Processing, Workshops and Phd Forum : [Proceedings]. Ieee International Symposium On Parallel & Distributed Processing, Workshops and Phd Forum. 2016: 89-100. PMID 27516922 DOI: 10.1109/IPDPSW.2016.130  0.371
2016 Earnest TM, Cole JA, Peterson JR, Hallock MJ, Kuhlman TE, Luthey-Schulten Z. Ribosome biogenesis in replicating cells: Integration of experiment and theory. Biopolymers. PMID 27294303 DOI: 10.1002/Bip.22892  0.333
2015 Earnest TM, Lai J, Chen K, Hallock MJ, Williamson JR, Luthey-Schulten Z. Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly. Biophysical Journal. 109: 1117-35. PMID 26333594 DOI: 10.1016/J.Bpj.2015.07.030  0.379
2015 Zhao H, Palencia A, Seiradake E, Ghaemi Z, Cusack S, Luthey-Schulten Z, Martinis S. Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism. Acs Chemical Biology. 10: 2277-85. PMID 26172575 DOI: 10.1021/Acschembio.5B00291  0.317
2015 Guzman I, Ghaemi Z, Baranger A, Luthey-Schulten Z, Gruebele M. Native conformational dynamics of the spliceosomal U1A protein. The Journal of Physical Chemistry. B. 119: 3651-61. PMID 25659967 DOI: 10.1021/Jp511760M  0.427
2015 Nguyen CT, Ngo T, Park S, Cox K, Ha T, Luthey-Schulten ZA, Kuhlman TE. Spatial Organization of Ribosome Biogenesis of Escherichia Coli Biophysical Journal. 108: 312a. DOI: 10.1016/J.Bpj.2014.11.1698  0.351
2015 Ghaemi Z, Guzman I, Gruebele M, Luthey-Schulten Z. Electrostatic Interaction Effects on the Binding of Spliceosomal U1A Protein-SL2 RNA Hairpin Biophysical Journal. 108: 15a. DOI: 10.1016/J.Bpj.2014.11.106  0.377
2014 Cole JA, Luthey-Schulten Z. Whole Cell Modeling: From Single Cells to Colonies. Israel Journal of Chemistry. 54: 1219-1229. PMID 26989262 DOI: 10.1002/Ijch.201300147  0.358
2014 Hallock MJ, Stone JE, Roberts E, Fry C, Luthey-Schulten Z. Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations. Parallel Computing. 40: 86-99. PMID 24882911 DOI: 10.1016/j.parco.2014.03.009  0.505
2014 Peterson JR, Labhsetwar P, Ellermeier JR, Kohler PR, Jain A, Ha T, Metcalf WW, Luthey-Schulten Z. Towards a computational model of a methane producing archaeum. Archaea (Vancouver, B.C.). 2014: 898453. PMID 24729742 DOI: 10.1155/2014/898453  0.339
2014 Kim H, Abeysirigunawarden SC, Chen K, Mayerle M, Ragunathan K, Luthey-Schulten Z, Ha T, Woodson SA. Protein-guided RNA dynamics during early ribosome assembly. Nature. 506: 334-8. PMID 24522531 DOI: 10.1038/Nature13039  0.395
2014 Earnest TM, Roberts E, Assaf M, Dahmen K, Luthey-Schulten Z. Corrigendum: DNA looping increases the range of bistability in a stochastic model of the lac genetic switch (2013 Phys. Biol. 10 026002) Physical Biology. 11: 029501. DOI: 10.1088/1478-3975/11/2/029501  0.517
2014 Labhsetwar P, Cole JA, Roberts E, Price ND, Luthey-Schulten ZA. 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) Proceedings of the National Academy of Sciences of the United States of America. 111. DOI: 10.1073/Pnas.1323512111  0.544
2014 Earnest TM, Luthey-Schulten Z. Coarse-Grained Simulations of Nucleoid Structure Biophysical Journal. 106: 79a. DOI: 10.1016/J.Bpj.2013.11.513  0.362
2014 Lai J, Chen K, Kim H, Ha T, Luthey-Schulten Z. Hierarchical Folding of the rRNA in the Early Assembly of the E. Coli Ribosomal Small Subunit Biophysical Journal. 106: 804a. DOI: 10.1016/J.Bpj.2013.11.4407  0.407
2014 Labhsetwar P, Cole J, Price N, Luthey-Schulten Z. Elucidating Metabolic Variability in Isogenic Microbial Populations Arising due to Noise in Protein Expression Biophysical Journal. 106: 644a. DOI: 10.1016/J.Bpj.2013.11.3564  0.313
2014 Chen K, Wang B, Fei J, Luthey-Schulten Z. Translation in the RNA World: Insight from the Proto-Ribosome Model Biophysical Journal. 106: 490a. DOI: 10.1016/J.Bpj.2013.11.2740  0.362
2014 Peterson JR, Labhsetwar P, Kohler P, Ellermeier J, Metcalf W, Jain A, Ha T, Luthey-Schulten Z. Modeling Metabolic Variability in Methanosarcina Acetivorans Biophysical Journal. 106: 380a. DOI: 10.1016/J.Bpj.2013.11.2148  0.362
2013 Lai J, Chen K, Luthey-Schulten Z. Structural intermediates and folding events in the early assembly of the ribosomal small subunit Journal of Physical Chemistry B. 117: 13335-13345. PMID 23972210 DOI: 10.1021/Jp404106R  0.407
2013 Assaf M, Roberts E, Luthey-Schulten Z, Goldenfeld N. Extrinsic noise driven phenotype switching in a self-regulating gene. Physical Review Letters. 111: 058102. PMID 23952448 DOI: 10.1103/Physrevlett.111.058102  0.553
2013 Labhsetwar P, Cole JA, Roberts E, Price ND, Luthey-Schulten ZA. 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. 110: 14006-11. PMID 23908403 DOI: 10.1073/Pnas.1222569110  0.541
2013 Li L, Palencia A, Lukk T, Li Z, Luthey-Schulten ZA, Cusack S, Martinis SA, Boniecki MT. Leucyl-tRNA synthetase editing domain functions as a molecular rheostat to control codon ambiguity in Mycoplasma pathogens. Proceedings of the National Academy of Sciences of the United States of America. 110: 3817-22. PMID 23431144 DOI: 10.1073/Pnas.1218374110  0.372
2013 Earnest TM, Roberts E, Assaf M, Dahmen K, Luthey-Schulten Z. DNA looping increases the range of bistability in a stochastic model of the lac genetic switch. Physical Biology. 10: 026002. PMID 23406725 DOI: 10.1088/1478-3975/10/2/026002  0.576
2013 Li L, Martinis SA, Luthey-Schulten Z. Capture and quality control mechanisms for adenosine-5′-triphosphate binding Journal of the American Chemical Society. 135: 6047-6055. PMID 23276298 DOI: 10.1021/Ja308044W  0.331
2013 Roberts E, Stone JE, Luthey-Schulten Z. Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation. Journal of Computational Chemistry. 34: 245-55. PMID 23007888 DOI: 10.1002/Jcc.23130  0.562
2013 Cole J, Hallock MJ, Labhsetwar P, Peterson JR, Stone JE, Luthey-Schulten Z. Stochastic Simulations of Cellular Processes: From Single Cells to Colonies Computational Systems Biology: From Molecular Mechanisms to Disease: Second Edition. 277-293. DOI: 10.1016/J.Bpj.2013.11.077  0.327
2013 Labhsetwar P, Cole J, Roberts E, Price N, Luthey-Schulten Z. Heterogenity in Protein Copy Numbers induces Metabolic Variability in Modeled E. coli Populations Biophysical Journal. 104: 495a. DOI: 10.1016/J.Bpj.2012.11.2731  0.559
2013 Luthey-Schulten Z. Stochastic Simulations of Cellular Processes in Bacteria Biophysical Journal. 104: 385a. DOI: 10.1016/J.Bpj.2012.11.2149  0.369
2012 Vanwart AT, Eargle J, Luthey-Schulten Z, Amaro RE. Exploring residue component contributions to dynamical network models of allostery. Journal of Chemical Theory and Computation. 8: 2949-2961. PMID 23139645 DOI: 10.1021/Ct300377A  0.784
2012 Eargle J, Luthey-Schulten Z. NetworkView: 3D display and analysis of protein·RNA interaction networks. Bioinformatics (Oxford, England). 28: 3000-1. PMID 22982572 DOI: 10.1093/Bioinformatics/Bts546  0.733
2012 Chen K, Eargle J, Lai J, Kim H, Abeysirigunawardena S, Mayerle M, Woodson S, Ha T, Luthey-Schulten Z. Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations. The Journal of Physical Chemistry. B. 116: 6819-31. PMID 22458631 DOI: 10.1021/Jp212614B  0.762
2012 Kim H, Abeysirigunawardena S, Mayerle M, Ragunathan K, Chen K, Eargle J, Luthey-Schulten Z, Woodson S, Ha T. Single Molecule Views of the Ribosome Assembly Biophysical Journal. 102: 645a. DOI: 10.1016/J.Bpj.2011.11.3512  0.756
2011 Assaf M, Roberts E, Luthey-Schulten Z. Determining the stability of genetic switches: explicitly accounting for mRNA noise. Physical Review Letters. 106: 248102. PMID 21770603 DOI: 10.1103/Physrevlett.106.248102  0.57
2011 Li L, Boniecki MT, Jaffe JD, Imai BS, Yau PM, Luthey-Schulten ZA, Martinis SA. Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites. Proceedings of the National Academy of Sciences of the United States of America. 108: 9378-83. PMID 21606343 DOI: 10.1073/Pnas.1016460108  0.303
2011 Roberts E, Magis A, Ortiz JO, Baumeister W, Luthey-Schulten Z. Noise contributions in an inducible genetic switch: a whole-cell simulation study. Plos Computational Biology. 7: e1002010. PMID 21423716 DOI: 10.1371/Journal.Pcbi.1002010  0.572
2011 Assaf M, Roberts E, Luthey-Schulten Z. Determining the stability of genetic switches: Explicitly accounting for mRNA noise Physical Review Letters. 106. DOI: 10.1103/PhysRevLett.106.248102  0.446
2010 Chen K, Eargle J, Sarkar K, Gruebele M, Luthey-Schulten Z. Functional role of ribosomal signatures. Biophysical Journal. 99: 3930-40. PMID 21156135 DOI: 10.1016/J.Bpj.2010.09.062  0.76
2010 Trabuco LG, Schreiner E, Eargle J, Cornish P, Ha T, Luthey-Schulten Z, Schulten K. The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. Journal of Molecular Biology. 402: 741-60. PMID 20691699 DOI: 10.1016/J.Jmb.2010.07.056  0.758
2010 Mathew DC, Luthey-Schulten Z. Influence of montmorillonite on nucleotide oligomerization reactions: a molecular dynamics study. Origins of Life and Evolution of the Biosphere : the Journal of the International Society For the Study of the Origin of Life. 40: 303-17. PMID 20213159 DOI: 10.1007/S11084-010-9207-0  0.738
2010 Black Pyrkosz A, Eargle J, Sethi A, Luthey-Schulten Z. Exit strategies for charged tRNA from GluRS. Journal of Molecular Biology. 397: 1350-71. PMID 20156451 DOI: 10.1016/J.Jmb.2010.02.003  0.744
2010 Alexander RW, Eargle J, Luthey-Schulten Z. Experimental and computational determination of tRNA dynamics. Febs Letters. 584: 376-86. PMID 19932098 DOI: 10.1016/J.Febslet.2009.11.061  0.757
2009 Butler T, Goldenfeld N, Mathew D, Luthey-Schulten Z. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 79: 060901. PMID 19658466 DOI: 10.1103/Physreve.79.060901  0.739
2009 Chen K, Roberts E, Luthey-Schulten Z. Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4. Bmc Evolutionary Biology. 9: 179. PMID 19640295 DOI: 10.1186/1471-2148-9-179  0.566
2009 Sethi A, Eargle J, Black AA, Luthey-Schulten Z. Dynamical networks in tRNA:protein complexes. Proceedings of the National Academy of Sciences of the United States of America. 106: 6620-5. PMID 19351898 DOI: 10.1073/Pnas.0810961106  0.778
2009 Roberts E, Stone JE, Sepúlveda L, Hwu WMW, Luthey-Schulten Z. Long time-scale simulations of in vivo diffusion using GPU hardware Ipdps 2009 - Proceedings of the 2009 Ieee International Parallel and Distributed Processing Symposium. DOI: 10.1109/IPDPS.2009.5160930  0.458
2009 Butler T, Goldenfeld N, Mathew D, Luthey-Schulten Z. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 79. DOI: 10.1103/PhysRevE.79.060901  0.717
2008 Roberts E, Sethi A, Montoya J, Woese CR, Luthey-Schulten Z. Molecular signatures of ribosomal evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 13953-8. PMID 18768810 DOI: 10.1073/Pnas.0804861105  0.705
2008 Mathew DC, Luthey-Schulten Z. On the physical basis of the amino acid polar requirement. Journal of Molecular Evolution. 66: 519-28. PMID 18443736 DOI: 10.1007/S00239-008-9073-9  0.731
2008 Eargle J, Black AA, Sethi A, Trabuco LG, Luthey-Schulten Z. Dynamics of Recognition between tRNA and elongation factor Tu. Journal of Molecular Biology. 377: 1382-405. PMID 18336835 DOI: 10.1016/J.Jmb.2008.01.073  0.796
2007 Amaro RE, Sethi A, Myers RS, Davisson VJ, Luthey-Schulten ZA. A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase. Biochemistry. 46: 2156-73. PMID 17261030 DOI: 10.1021/Bi061708E  0.681
2007 Pogorelov TV, Autenrieth F, Roberts E, Luthey-Schulten ZA. Cytochrome c(2) Exit Strategy: Dissociation Studies and Evolutionary Implications. The Journal of Physical Chemistry. B. 111: 618-34. PMID 17228920 DOI: 10.1021/Jp064973I  0.753
2006 Roberts E, Eargle J, Wright D, Luthey-Schulten Z. MultiSeq: unifying sequence and structure data for evolutionary analysis. Bmc Bioinformatics. 7: 382. PMID 16914055 DOI: 10.1186/1471-2105-7-382  0.79
2006 Eargle J, Luthey-Schulten Z. Visualizing the dual space of biological molecules. Computational Biology and Chemistry. 30: 219-26. PMID 16675303 DOI: 10.1016/J.Compbiolchem.2006.01.004  0.731
2006 Eargle J, Wright D, Luthey-Schulten Z. Multiple Alignment of protein structures and sequences for VMD. Bioinformatics (Oxford, England). 22: 504-6. PMID 16339280 DOI: 10.1093/Bioinformatics/Bti825  0.75
2005 O'Donoghue P, Sethi A, Woese CR, Luthey-Schulten ZA. The evolutionary history of Cys-tRNACys formation. Proceedings of the National Academy of Sciences of the United States of America. 102: 19003-8. PMID 16380427 DOI: 10.1073/Pnas.0509617102  0.758
2005 Myers RS, Amaro RE, Luthey-Schulten ZA, Davisson VJ. Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase. Biochemistry. 44: 11974-85. PMID 16142895 DOI: 10.1021/Bi050706B  0.558
2005 Amaro RE, Myers RS, Davisson VJ, Luthey-Schulten ZA. Structural elements in IGP synthase exclude water to optimize ammonia transfer. Biophysical Journal. 89: 475-87. PMID 15849257 DOI: 10.1529/Biophysj.104.058651  0.577
2005 Sethi A, O'Donoghue P, Luthey-Schulten Z. Evolutionary profiles from the QR factorization of multiple sequence alignments. Proceedings of the National Academy of Sciences of the United States of America. 102: 4045-50. PMID 15741270 DOI: 10.1073/Pnas.0409715102  0.739
2005 O'Donoghue P, Luthey-Schulten Z. Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information Journal of Molecular Biology. 346: 875-894. PMID 15713469 DOI: 10.1016/J.Jmb.2004.11.053  0.69
2004 Autenrieth F, Tajkhorshid E, Baudry J, Luthey-Schulten Z. Classical force field parameters for the heme prosthetic group of cytochrome c Journal of Computational Chemistry. 25: 1613-1622. PMID 15264255 DOI: 10.1002/Jcc.20079  0.531
2004 Pogorelov TV, Luthey-Schulten Z. Variations in the fast folding rates of the lambda-repressor: a hybrid molecular dynamics study. Biophysical Journal. 87: 207-14. PMID 15240458 DOI: 10.1529/Biophysj.104.042861  0.709
2004 Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG. Water in protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 101: 3352-7. PMID 14988499 DOI: 10.1073/Pnas.0307851100  0.546
2004 Fujitsuka Y, Takada S, Luthey-Schulten ZA, Wolynes PG. Optimizing physical energy functions for protein folding. Proteins. 54: 88-103. PMID 14705026 DOI: 10.1002/Prot.10429  0.576
2004 Autenrieth F, Tajkhorshid E, Schulten K, Luthey-Schulten Z. Role of water in transient cytochrome c 2 docking Journal of Physical Chemistry B. 108: 20376-20387. DOI: 10.1021/Jp047994Q  0.572
2004 Amaro R, Luthey-Schulten Z. Molecular dynamics simulations of substrate channeling through an α-β Barrel protein Chemical Physics. 307: 147-155. DOI: 10.1016/J.Chemphys.2004.05.019  0.567
2003 O'Donoghue P, Luthey-Schulten Z. Evolution of Structure in Aminoacyl-tRNA Synthetases Microbiology and Molecular Biology Reviews. 67: 550-573. PMID 14665676 DOI: 10.1128/Mmbr.67.4.550-573.2003  0.718
2003 Amaro R, Tajkhorshidt E, Luthey-Schulten Z. Developing an energy landscape for the novel function of a (β/α)8 barrel: Ammonia conduction through HisF Proceedings of the National Academy of Sciences of the United States of America. 100: 7599-7604. PMID 12799468 DOI: 10.1073/Pnas.1331150100  0.562
2003 Wang J, Luthey-Schulten ZA, Suslick KS. Is the olfactory receptor a metalloprotein? Proceedings of the National Academy of Sciences of the United States of America. 100: 3035-9. PMID 12610211 DOI: 10.1073/Pnas.262792899  0.326
2003 Hardin C, Eastwood MP, Prentiss MC, Luthey-Schulten Z, Wolynes PG. Associative memory Hamiltonians for structure prediction without homology: alpha/beta proteins. Proceedings of the National Academy of Sciences of the United States of America. 100: 1679-84. PMID 12554830 DOI: 10.1073/Pnas.252753899  0.55
2003 Eastwood MP, Hardin C, Luthey-Schulten Z, Wolynes PG. Statistical mechanical refinement of protein structure prediction schemes. II. Mayer cluster expansion approach Journal of Chemical Physics. 118: 8500-8512. DOI: 10.1063/1.1565106  0.537
2002 Hardin C, Pogorelov TV, Luthey-Schulten Z. Ab initio protein structure prediction. Current Opinion in Structural Biology. 12: 176-81. PMID 11959494 DOI: 10.1016/S0959-440X(02)00306-8  0.724
2002 Hardin C, Eastwood MP, Prentiss M, Luthey-Schulten Z, Wolynes PG. Folding funnels: the key to robust protein structure prediction. Journal of Computational Chemistry. 23: 138-46. PMID 11913379 DOI: 10.1002/Jcc.1162  0.553
2002 Eastwood MP, Hardin C, Luthey-Schulten Z, Wolynes PG. Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach Journal of Chemical Physics. 117: 4602-4615. DOI: 10.1063/1.1494417  0.509
2001 O'Donoghue P, Amaro RE, Luthey-Schulten Z. On the structure of hisH: protein structure prediction in the context of structural and functional genomics. Journal of Structural Biology. 134: 257-68. PMID 11551184 DOI: 10.1006/Jsbi.2001.4390  0.763
2001 Eastwood MP, Hardin C, Luthey-Schulten Z, Wolynes PG. Evaluating protein structure-prediction schemes using energy landscape theory Ibm Journal of Research and Development. 45: 475-497. DOI: 10.1147/Rd.453.0475  0.519
2000 Hardin C, Eastwood MP, Luthey-Schulten Z, Wolynes PG. Associative memory hamiltonians for structure prediction without homology: alpha-helical proteins. Proceedings of the National Academy of Sciences of the United States of America. 97: 14235-40. PMID 11114172 DOI: 10.1073/pnas.230432197  0.482
1999 Hardin C, Luthey-Schulten Z, Wolynes PG. Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides. Proteins. 34: 281-94. PMID 10024016 DOI: 10.1002/(Sici)1097-0134(19990215)34:3<281::Aid-Prot2>3.0.Co;2-2  0.563
1999 Takada S, Luthey-Schulten Z, Wolynes PG. Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer The Journal of Chemical Physics. 110: 11616-11629. DOI: 10.1063/1.479101  0.55
1998 Koretke KK, Luthey-Schulten Z, Wolynes PG. Self-consistently optimized energy functions for protein structure prediction by molecular dynamics. Proceedings of the National Academy of Sciences of the United States of America. 95: 2932-7. PMID 9501193 DOI: 10.1073/Pnas.95.6.2932  0.567
1997 Onuchic JN, Luthey-Schulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annual Review of Physical Chemistry. 48: 545-600. PMID 9348663 DOI: 10.1146/Annurev.Physchem.48.1.545  0.561
1997 Panchenko AR, Luthey-Schulten Z, Cole R, Wolynes PG. The foldon universe: a survey of structural similarity and self-recognition of independently folding units. Journal of Molecular Biology. 272: 95-105. PMID 9299340 DOI: 10.1006/Jmbi.1997.1205  0.549
1997 Haney P, Konisky J, Koretke KK, Luthey-Schulten Z, Wolynes PG. Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus. Proteins. 28: 117-30. PMID 9144797 DOI: 10.1002/(Sici)1097-0134(199705)28:1<117::Aid-Prot12>3.0.Co;2-M  0.561
1997 Panchenko AR, Luthey-Schulten Z, Wolynes PG. Foldons as independently folding units of proteins Physica D: Nonlinear Phenomena. 107: 312-315. DOI: 10.1016/S0167-2789(97)00098-5  0.567
1996 Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG. Protein folding funnels: the nature of the transition state ensemble. Folding & Design. 1: 441-50. PMID 9080190 DOI: 10.1016/S1359-0278(96)00060-0  0.539
1996 Wolynes PG, Luthey-Schulten Z, Onuchic JN. Fast-folding experiments and the topography of protein folding energy landscapes Chemistry and Biology. 3: 425-432. PMID 8807873 DOI: 10.1016/S1074-5521(96)90090-3  0.54
1996 Koretke KK, Luthey-Schulten Z, Wolynes PG. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. Protein Science : a Publication of the Protein Society. 5: 1043-59. PMID 8762136 DOI: 10.1002/Pro.5560050607  0.527
1996 Panchenko AR, Luthey-Schulten Z, Wolynes PG. Foldons, protein structural modules, and exons. Proceedings of the National Academy of Sciences of the United States of America. 93: 2008-13. PMID 8700876 DOI: 10.1073/Pnas.93.5.2008  0.558
1995 Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND. Toward an outline of the topography of a realistic protein-folding funnel. Proceedings of the National Academy of Sciences of the United States of America. 92: 3626-30. PMID 7724609 DOI: 10.1073/Pnas.92.8.3626  0.57
1995 Luthey-Schulten Z, Ramirez BE, Wolynes PG. Helix-Coil, Liquid Crystal, and Spin Glass Transitions of a Collapsed Heteropolymer The Journal of Physical Chemistry. 99: 2177-2185. DOI: 10.1021/J100007A057  0.497
1993 Goldstein RA, Katzenellenbogen JA, Luthey-Schulten ZA, Seielstad DA, Wolynes PG. Three-dimensional model for the hormone binding domains of steroid receptors. Proceedings of the National Academy of Sciences of the United States of America. 90: 9949-53. PMID 8234340 DOI: 10.1073/Pnas.90.21.9949  0.526
1992 Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Optimal protein-folding codes from spin-glass theory. Proceedings of the National Academy of Sciences of the United States of America. 89: 4918-22. PMID 1594594 DOI: 10.1073/Pnas.89.11.4918  0.519
1992 Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proceedings of the National Academy of Sciences of the United States of America. 89: 9029-33. PMID 1409599 DOI: 10.1073/Pnas.89.19.9029  0.55
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