| 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 |
0.418 |
|
| 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 |
0.61 |
|
| 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 |
0.758 |
|
| 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 |
0.303 |
|
| 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 |
0.345 |
|
| 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 |
0.337 |
|
| 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 |
0.43 |
|
| 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 |
0.316 |
|
| 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 |
0.363 |
|
| 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 |
0.378 |
|
| 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 |
0.501 |
|
| 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 |
0.513 |
|
| 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 |
0.541 |
|
| 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 |
0.408 |
|
| 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 |
0.312 |
|
| 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 |
0.363 |
|
| 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 |
0.55 |
|
| 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 |
0.538 |
|
| 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 |
0.371 |
|
| 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 |
0.574 |
|
| 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 |
0.559 |
|
| 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 |
0.556 |
|
| 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 |
0.781 |
|
| 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 |
0.761 |
|
| 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 |
0.755 |
|
| 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 |
0.568 |
|
| 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 |
0.569 |
|
| 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 |
0.442 |
|
| 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 |
0.757 |
|
| 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 |
0.735 |
|
| 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 |
0.743 |
|
| 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 |
0.736 |
|
| 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 |
0.563 |
|
| 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 |
0.777 |
|
| 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 |
0.454 |
|
| 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 |
0.713 |
|
| 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 |
0.702 |
|
| 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 |
0.727 |
|
| 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 |
0.795 |
|
| 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 |
0.675 |
|
| 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 |
0.742 |
|
| 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 |
0.788 |
|
| 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 |
0.749 |
|
| 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 |
0.547 |
|
| 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 |
0.566 |
|
| 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 |
0.729 |
|
| 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 |
0.675 |
|
| 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 |
0.525 |
|
| 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 |
0.693 |
|
| 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 |
0.542 |
|
| 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 |
0.573 |
|
| 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 |
0.567 |
|
| 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 |
0.555 |
|
| 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 |
0.704 |
|
| 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 |
0.551 |
|
| 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 |
0.546 |
|
| 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 |
0.533 |
|
| 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 |
0.707 |
|
| 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 |
0.549 |
|
| 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 |
0.506 |
|
| 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 |
0.751 |
|
| 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 |
0.516 |
|
| 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 |
0.478 |
|
| 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 |
0.56 |
|
| 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 |
0.547 |
|
| 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 |
0.563 |
|
| 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 |
0.558 |
|
| 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 |
0.546 |
|
| 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 |
0.558 |
|
| 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 |
0.564 |
|
| 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 |
0.537 |
|
| 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 |
0.536 |
|
| 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 |
0.523 |
|
| 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 |
0.555 |
|
| 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 |
0.567 |
|
| 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 |
0.494 |
|
| 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 |
0.523 |
|
| 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 |
0.516 |
|
| 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 |
0.546 |
|
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