Publications

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Visualizing ligand molecules in Twilight electron density.
Weichenberger CX, Pozharski E, Rupp B. 2013. Visualizing ligand molecules in Twilight electron density. Acta crystallographica. Section F, Structural biology and crystallization communications 69(Pt 2): 195-200. DOI: 10.1107/S1744309112044387
Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures.
Pozharski E, Weichenberger CX, Rupp B. 2013. Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures. Acta crystallographica. Section D, Biological crystallography 69(Pt 2): 150-67. DOI: 10.1107/S0907444912044423
Thermococcus kodakarensis DNA replication.
Li Z, Kelman LM, Kelman Z. 2013. Thermococcus kodakarensis DNA replication. Biochemical Society transactions 41(1): 332-8. DOI: 10.1042/BST20120303
Six-site polarizable model of water based on the classical Drude oscillator.
Yu W, Lopes PE, Roux B, MacKerell AD. 2013. Six-site polarizable model of water based on the classical Drude oscillator. The Journal of chemical physics 138(3): 034508. DOI: 10.1063/1.4774577
Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography.
Wang X, Xu F, Liu J, Gao B, Liu Y, Zhai Y, Ma J, Zhang K, Baker TS, Schulten K, et al. 2013. Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography. PLoS pathogens 9(1): e1003132. DOI: 10.1371/journal.ppat.1003132
Autonomous bacterial localization and gene expression based on nearby cell receptor density.
Wu HC, Tsao CY, Quan DN, Cheng Y, Servinsky MD, Carter KK, Jee KJ, Terrell JL, Zargar A, Rubloff GW, et al. 2013. Autonomous bacterial localization and gene expression based on nearby cell receptor density. Molecular systems biology 9: 636. DOI: 10.1038/msb.2012.71
A unique IBMPFD-related P97/VCP mutation with differential binding pattern and subcellular localization.
Erzurumlu Y, Kose FA, Gozen O, Gozuacik D, Toth EA, Ballar P. 2013. A unique IBMPFD-related P97/VCP mutation with differential binding pattern and subcellular localization. The international journal of biochemistry & cell biology 45(4): 773-82. DOI: 10.1016/j.biocel.2013.01.006
Effects of gadolinium chelate on the evolution of the nanoscale structure in peptide hydrogels.
Taraban MB, Weerasekare M, Trewhella J, Shi X, Jeong EK, Yu YB. 2012. Effects of gadolinium chelate on the evolution of the nanoscale structure in peptide hydrogels. Biopolymers 98(1): 50-8. DOI: 10.1002/bip.21689
Reverse engineering to suggest biologically relevant redox activities of phenolic materials.
Kim E, Gordonov T, Liu Y, Bentley WE, Payne GF. 2013. Reverse engineering to suggest biologically relevant redox activities of phenolic materials. ACS chemical biology 8(4): 716-24. DOI: 10.1021/cb300605s
Further studies with isolated absolute infrared spectra of bacteriorhodopsin photocycle intermediates: conformational changes and possible role of a new proton-binding center.
Hendler RW, Meuse CW, Smith PD, Kakareka JW. 2013. Further studies with isolated absolute infrared spectra of bacteriorhodopsin photocycle intermediates: conformational changes and possible role of a new proton-binding center. Applied spectroscopy 67(1): 73-85. DOI: 10.1366/12-06662
Amplified and in situ detection of redox-active metabolite using a biobased redox capacitor.
Kim E, Gordonov T, Bentley WE, Payne GF. 2013. Amplified and in situ detection of redox-active metabolite using a biobased redox capacitor. Analytical chemistry 85(4): 2102-8. DOI: 10.1021/ac302703y
Biofabricated film with enzymatic and redox-capacitor functionalities to harvest and store electrons.
Liba BD, Kim E, Martin AN, Liu Y, Bentley WE, Payne GF. 2013. Biofabricated film with enzymatic and redox-capacitor functionalities to harvest and store electrons. Biofabrication 5(1): 015008. DOI: 10.1088/1758-5082/5/1/015008
Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1.
Lai Y, Diao J, Liu Y, Ishitsuka Y, Su Z, Schulten K, Ha T, Shin YK. 2013. Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1. Proceedings of the National Academy of Sciences of the United States of America 110(4): 1333-8. DOI: 10.1073/pnas.1218818110
In vivo screening of S100B inhibitors for melanoma therapy.
Zimmer DB, Lapidus RG, Weber DJ. 2013. In vivo screening of S100B inhibitors for melanoma therapy. Methods in molecular biology (Clifton, N.J.) 963: 303-17. DOI: 10.1007/978-1-62703-230-8_18
Quantifying the cluster of differentiation 4 receptor density on human T lymphocytes using multiple reaction monitoring mass spectrometry.
Wang M, He HJ, Turko IV, Phinney KW, Wang L. 2013. Quantifying the cluster of differentiation 4 receptor density on human T lymphocytes using multiple reaction monitoring mass spectrometry. Analytical chemistry 85(3): 1773-7. DOI: 10.1021/ac3031306