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

81 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
2015 Peterson JR, Cole JA, Fei J, Ha T, Luthey-Schulten ZA. Effects of DNA replication on mRNA noise. Proceedings of the National Academy of Sciences of the United States of America. PMID 26669443 DOI: 10.1073/pnas.1516246112  0.52
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  0.92
2015 Cole JA, Kohler L, Hedhli J, Luthey-Schulten Z. Spatially-resolved metabolic cooperativity within dense bacterial colonies. Bmc Systems Biology. 9: 15. PMID 25890263 DOI: 10.1186/s12918-015-0155-1  0.92
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  0.92
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: 2277-2285. DOI: 10.1021/acschembio.5b00291  0.92
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  0.92
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  0.92
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  0.92
2014 Cole JA, Luthey-Schulten Z. Whole cell modeling: From single cells to colonies Israel Journal of Chemistry. DOI: 10.1002/ijch.201300147  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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/B978-0-12-405926-9.00013-7  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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.  0.92
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  0.92
2000 O'Donoghue P, Luthey-Schulten ZA. Barriers to forced transitions in polysaccharides Journal of Physical Chemistry B. 104: 10398-10405.  0.92
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  0.92
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 Journal of Chemical Physics. 110: 11616-11629.  0.92
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  0.92
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  0.92
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  0.92
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  0.92
1997 Panchenko AR, Luthey-Schulten Z, Wolynes PG. Foldons as independently folding units of proteins Physica D: Nonlinear Phenomena. 107: 312-315.  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
1995 Luthey-Schulten Z, Ramirez BE, Wolynes PG. Helix-coil, liquid crystal, and spin glass transitions of a collapsed heteropolymer Journal of Physical Chemistry. 99: 2177-2185.  0.92
1995 Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Bayesian approach to sequence alignment algorithms for protein structure recognition Proceedings of the Hawaii International Conference On System Sciences. 5: 306-315.  0.92
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  0.92
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  0.92
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  0.92
1990 Draves JA, Luthey-Schulten Z, Liu WL, Lisy JM. Gas-phase methanol solvation of Cs+: Vibrational spectroscopy and Monte Carlo simulation The Journal of Chemical Physics. 93: 4589-4602.  0.92
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