Center for Eukaryotic Structural Genomics Publications

   | PDF of Publications | Home |     Total:  130 Publications      Last Updated August 27, 2008

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  • KEY || BI = Bioinformatics || PP = Protein Production | CODE = PSI Phase / Year / Quarter when reported / in PSI Knowledgebase (K)
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AUTHORS YEAR TITLE JOURNAL/BOOK VOL/ISSUE/PAGES TEAM TYPE PDF CODE PUBMED/PUBMED CENTRAL
Aceti, D.J., Bitto, E., Yakunin, A.F., Proudfoot, M., Bingman, C.A., Frederick, R.O., Sreenath, H.K., Vojtik, F.C., Wrobel, R.L., Fox, B.G., Markley, J.L., and Phillips, G.N., Jr. 2008 Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000 Proteins 73(1):241-53 X-ray Structural X 233K PMID:18433060
Aceti, D.J., Blommel, P.G., Endo, Y., Fox, B.G., Frederick, R.O., Hegeman, A.D., Jeon, W.B., Kimball, T.L., Lee, J.M., Newman, C.S., Peterson, F.C., Sawasaki, T., Seder, K.D., Sussman, M.R., Ulrich, E.L., Wrobel, R.L., Thao, S., Vinarov, D.A., Volkman, B.F., and Zhao, Q. 2003 Role of nucleic acid and protein manipulation technologies in high-throughput structural biology efforts Biopolymers, Wiley-VCH, Weinheim 8:469-96 PP Method X 1 Not Applicable
Allard, S.T.M., Bingman, C.A., Johnson, K.A., Wesenberg, G.E., Bitto, E., Jeon, W.B., and Phillips, G.N., Jr. 2005 Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana Acta Crystallograph Sect F Struct Biol Cryst Commun 61(Pt 7):647-50 X-ray Structural X 1K PMID:16511118
PMCID:PMC1952470
Aranda, R., Worley, C.E., Liu, M., Bitto, E., Cates, M.S., Olson, J.S., Lei, B., and Phillips, G.N., Jr. 2007 Bis-methionyl coordination in the crystal structure of the heme-binding domain of the streptococcal cell surface protein Shp J Mol Biol 374(2):374-83 X-ray Structural X 232K PMID:17920629
PMCID:PMC2386982
(on 11/23/08)
Arangarasan, R., and Phillips, G.N., Jr. 2002 Modular approach of multimodal integration in a virtual environment Proceedings of the Fourth IEEE International Conference on Multimodal Interfaces (ICMI '02), IEEE Computer Society X-ray Method X 1K Not Applicable
Bae, E., Bannen, R.M., and Phillips, G.N., Jr. 2008 Bioinformatic method for protein thermal stabilization by structural entropy optimization Proc Natl Acad Sci USA 105(28):9595-7 X-ray Methods X 234 PMID:18621726
Bae, E., Bingman, C.A., Bitto, E., Aceti, D.J., and Phillips, G.N., Jr. 2008 Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase Proteins (in press) X-ray Structural 231K
Bae, E., Bingman, C.A., Bitto, E., Aceti, D.J., and Phillips, G.N., Jr. 2008 Crystal structure of Homo sapiens protein LOC79017 Proteins 70(2):588-91 X-ray Structural X 231K PMID:17932939
Bae, E., Reiter, N.J., Bingman, C.A., Kwan, S.S., Lee, D., Phillips, G.N., Jr., Butcher, S.E., and Brow, D.A. 2007 Structure and interactions of the first three RNA recognition motifs of splicing factor prp24 J Mol Biol 367(5):1447-58 X-ray Structural X 224K PMID:17320109
PMCID:PMC1939982
Bailey, L.J., Elsen, N.L., Pierce, B.S., and Fox, B.G. 2008 Soluble expression and purification of the oxidoreductase component of tuluene 4-monooxygenase Prot Expr Purif 57(1):9-16 Cloning Method X 233K PMID:17964805
Bannen, R.M., Bingman, C.A., and Phillips, G.N., Jr. 2008 Effect of low-complexity regions on protein structure determination JSFG 8(4):217-26 X-ray Method X 233K PMID:18302007
Bianchetti, C.M., Yi, L., Ragsdale, S.W., and Phillips, G.N., Jr. 2007 Comparison of apo- and heme-bound crystal structures of a truncated human heme oxygenase-2 J Biol Chem 282(52):37624-31 X-ray Structural X 231K PMID:17965015
Bingman, C.A., Johnson, K.A., Peterson, F.C., Frederick, R.O., Zhao, Q., Thao, S., Fox, B.G., Volkman, B.F., Jeon, W.B., Smith, D.W., Newman, C.S., Ulrich, E.L., Hegeman, A.D., Sussman, M.R., Markley, J.L., and Phillips, G.N., Jr. 2004 Crystal structure of the protein from gene At3g17210 of Arabidopsis thaliana Proteins 57(1):218-20 X-ray Structural X 1K PMID:15326607
Bitto, E., Bingman, C.A., Allard, S.T.M., Wesenberg, G.E., Aceti, D.J., Wrobel, R.L., Frederick, R.O., Sreenath, H.K., Vojtik, F.C., Jeon, W.B., Newman, C.S., Primm, J.G., Sussman, M.R., Fox, B.G., Markley, J.L., and Phillips, G.N., Jr. 2005 The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative FeII/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana Acta Crystallograph Sect F Struct Biol Cryst Commun 61(Pt 5):469-72 X-ray Structural X 1K PMID:16511070
PMCID:PMC1952295
Bitto, E., Bingman, C.A., Allard, S.T.M., Wesenberg, G.E., and Phillips, G.N., Jr. 2005 The structure at 1.7 A resolution of the protein product of the At2g17340 gene from Arabidopsis thaliana Acta Crystallograph Sect F Struct Biol Cryst Commun 61(Pt 7):630-5 X-ray Structural X 1K PMID:16511115
PMCID:PMC1952457
Bitto, E., Bingman, C.A., Bittova, L., Kondrashov, D.A., Bannen, R.M., Fox, B.G., Markley, J.L., Phillips, G.N., Jr. 2008 Structure of human J-type co-chaperone HscB reveals a tetracysteine metal binding domain J Biol Chem (in press) X-ray Structural X 241 PMID:18713742
Bitto, E., Bingman, C.A., Bittova, L., Houston, N.I., Bosten, R.S., Fox, B.G., and Phillips, G.N., Jr. 2008 X-ray structure of ILL2, and auxin-conjugate amidohydrolase from Arabidopsis thaliana Proteins (in press) X-ray Structural 234K PMID:18543330
Bitto, E., Bingman, C.A., Kondrashov, D.A., McCoy, J.G., Bannen, R.M., Wesenberg, G.E., and Phillips, G.N., Jr. 2008 Structure and dynamics of gamma-SNAP: insight into flexibility of proteins from the SNAP family Proteins 70(1):93-104 X-ray Structural X 223K PMID:17634982
Bitto, E., Bingman, C.A., McCoy, J.G., Allard, S.T.M., Wesenberg, G.E., and Phillips, G.N., Jr. 2005The structure at 1.6 A resolution of the protein product of the At4g34215 gene from Arabidopsis thaliana Acta Crystallogr D Biol Crystallogr 61(Pt 12):1655-61 X-rayStructural X 21K PMID:16301800
Bitto, E., Bingman, C.A., Robinson, H., Allard, S.T.M., Wesenberg, G.E., and Phillips, G.N., Jr. 2005 The crystal structure at 2.5 A resolution of human basophilic leukemia expressed protein BLES03 Acta Crystallograph Sect F Struct Biol Cryst Commun 61(Pt 9):812-7 X-ray Structural X 1K PMID:16511166
PMCID:PMC1978119
Bitto, E., Bingman, C.A., Wesenberg, G.E., McCoy, J.G., and Phillips, G.N., Jr. 2006 Structure of pyrimidine 5'-nucleotidase type 1: Insight into mechanism of action and inhibition during lead poisoning J Biol Chem 281(29):20521-9 X-ray Structural X 21K PMID:16672222
Bitto, E., Bingman, C.A., Wesenberg, G.E., McCoy, J.G., and Phillips, G.N., Jr. 2007 Structure of aspartoacylase, the brain enzyme impaired in Canavan disease Proc Natl Acad Sci USA 104(2):456-61 X-ray Structural X 222K PMID:17194761
PMCID:PMC1766406
Bitto, E., Huang, Y., Bingman, C.A., Singh, S., Thorson, J.S., and Phillips, G.N., Jr. 2008 The structure of flavin-dependent tryptophan 7-halogenase RebH Proteins 70(1):289-93 X-ray Structural X 231K PMID:17876823
Blommel, P.G., Becker, K.J., Duvnjak, P., and Fox, B.G. 2007 Enhanced bacterial protein expression during auto-induction obtained by alteration of lac repressor dosage and medium composition Biotechnol Prog23(3):585-98 Cloning Method X 222K PMID:17506520
Blommel, P.G., and Fox, B.G. 2005 Fluorescence anisotropy for proteolysis of specifically labeled fusion proteins Anal Biochem 336(1):75-86 Cloning Method X 1K PMID:15582561
Blommel, P.G., and Fox, B.G. 2007 A combined approach to improving large-scale production of tobacco etch virus protease Prot Expr Purif55(1P):53-68 Cloning Method X 222K PMID:17543538
PMCID:PMC2047602
(on 09/01/08)
Blommel, P.G., Martin, P.A., Wrobel, R.L., Steffen, E., and Fox, B.G. 2006 High-efficiency single-step production of expression plasmids from cDNA clones using the FlexiVector cloning system Prot Expr Purif 47(2):562-70 X-ray Method X 21K PMID:16377204
Blommel, P.G., Smith, D.W., Bingman, C.A., Dyer, D.H., Rayment, I., Holden, H.M., Fox, B.G., and Phillips, G.N., Jr. 2004 Crystal structure of gene locus At3g16990 from Arabidopsis thaliana Proteins 57(1):221-2 X-ray Structural X 1K PMID:15326608
Chae, Y.K., Im, H., Zhao, Q., Doelling, J.H., Vierstra, R.D., and Markley, J.L. 2004 Prevention of aggregation after refolding by balanced stabilization-destabilization: production of the Arabidopsis thaliana protein APG8a (At4g21980) for NMR structure determination Prot Expr Purif 34(2):280-3 NMR Structural X 1K PMID:15003262
Chae, Y.K., Lee, K., and Markley, J.L. 2005 1H, 15N, and 13C resonance assignments of a protein involved in the autophagy process, At4g21980.1 from Arabidopsis thaliana J Biomol NMR 32(4):337 NMR Structural X 21K PMID:16211491
Cornilescu, C.C., Porter, F.W., Zhao, K.Q., Palmenberg, A.C., and Markley, J.L. 2008 NMR structure of the mengovirus Leader protein zinc-finger domain FEBS Lett 582(6):896-900 NMR Structural X 233K PMID:18291103
Cornilescu, G., Bahrami, A., Tonelli, M., Markley, J.L., and Eghbalnia, H.R. 2007 HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections J Biomol NMR 38(4):341-51 NMR Method X 231K PMID:17610130
Cornilescu, G., Cornilescu, C.C., Zhao, Q., Frederick, R.O., Peterson, F.C., Thao, S., and Markley, J.L. 2004 Solution structure of a homodimeric hypothetical protein, At5g22580, a structural genomics target from Arabidopsis thaliana J Biomol NMR 29(3):387-90 NMR Structural X 1K PMID:15213437
Cornilescu, G., Hadley, E.B., Woll, M.G., Markley, J.L., Gellman, S.H., and Cornilescu, C.C. 2007 Solution structure of a small protein containing a fluorinated side chain in the core Protein Sci 16(1):14-9 NMR Structural X 223K PMID:17123960
PMCID:PMC2222841
Cornilescu, G., Vinarov, D.A., Tyler, E.M., Markley, J.L., and Cornilescu, C.C. 2006Solution structure of a single-domain thiosulfate sulfurtransferase from Arabidopsis thaliana Protein Sci 15(12):2836-41 NMR Structural X 21K PMID:17088324
PMCID:PMC2242445
Davis, C.A., Bingman, C.A., Landick, R., Record, M.T., Jr., and Saecker, R.M. 2007 Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase Proc Natl Acad Sci USA 104(19):7833-8 X-ray Method X 233K PMID:17470797
PMCID:PMC1876533
de la Cruz, N.B., Peterson, F.C., Lytle, B.L., and Volkman, B.F. 2007 Solution structure of a membrane-anchored ubiquitin-fold (MUB) protein from Homo sapiens Protein Sci 16(7):1479-84 NMR Structural X 224K PMID:17567738
PMCID:PMC2206703
de la Cruz, N.B., Peterson, F.C., and Volkman, B.F. 2008 Solution structure of At3g28950 from Arabidopsis thaliana Proteins 71(2):546-51 NMR Structural X 233K PMID:18214976
Dias, J.S., Macedo, A.L., Ferreira, G.C., Peterson, F.C., Volkman, B.F., and Goodfellow, B.J. 2006 The first structure from the SOUL/HBP family of heme-binding proteins, murine P22HBP J Biol Chem 281(42):31553-61 NMR Structural X 21K PMID:16905545
DiMaio, F., Shavlik, J.D., and Phillips, G.N., Jr. 2006 A probabilistic approach to protein backbone tracing in electron density maps Bioinformatics 22(14):e81-9 BI Method X 21K PMID:16873525
DiMaio, F., Soni, A., Phillips, G.N., Jr., and Shavlik, J. 2008 Spherical-harmonic decomposition for molecular recognition in electron-density maps IEEE-BIBM Conference Proceedings (in press) X-ray Method X 231K
DiMaio, F., Soni, A., Phillips, G.N., Jr., and Shavlik, J.W. 2007 Creating all-atom protein models from electron-density maps using particle-filtering methods Bioinformatics23(21):2851-8 BI Method X 222K PMID:17933855
Doreleijers, J.F., Mading, S., Maziuk, D., Sojourner, K., Yin, L., Zhu, J., Markley, J.L., and Ulrich, E.L. 2004 BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank J Biomol NMR 26(2):139-46 BI Method X 1K PMID:12766409
Doreleijers, J.F., Nederveen, A.J., Vranken, W., Lin, J., Bonvin, A.M.J.J., Kaptein, R., Markley, J.L., and Ulrich, E.L. 2005 BioMagResBank databases DOCR and FRED with converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures J Biomol NMR 32(1):1-12 BI Method X 1K PMID:16041478
Eghbalnia, H.R., Bahrami, A., Tonelli, M., Hallenga, K., and Markley, J.L. 2005 High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection J Am Chem Soc 127(36):12528-36 NMR Method X 21K PMID:16144400
PMCID:in progress
Eghbalnia, H.R., Bahrami, A., Wang, L., Assadi, A., and Markley, J.L. 2005 Probabilistic Identification of Spin Systems and Their Assignments including Coil-Helix Inference as Output (PISTACHIO) J Biomol NMR 32(3):219-33 NMRMethod X 21K PMID:16132822
Eghbalnia, H.R., Wang, L., Bahrami, A., Assadi, A., and Markley, J.L. 2005 Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements J Biomol NMR 32(1):71-81 NMR Method X 1K PMID:16041485
Fogh, R., Ionides, J., Ulrich, E.L., Boucher, W., Vranken, W., Linge, J.P., Habeck, M., Rieping, W., Bhat, T.N., Westbrook, J., Henrick, K., Gilliland, G., Berman, H., Thornton, J.T., Nilges, M., Markley, J.L., and Laue, E. 2002 The CCPN project: an interim report on a data model for the NMR community Nature Struct Biol9(6):416-8 NMR Method X 1K PMID:12032555
Fox, B.G., Goulding, C., Malkowski, M.G., Stewart, L., and Deacon, A. 2008 Structural genomics: from genes to structures with valuable materials and many questions in between Nat Methods 5(2):129-32 None Method X 233K PMID:18235432
Fox, B.G., Malone, T.E., Aceti, D.J., Bingman, C.A., Blommel, P.G., Buchan, B.W., Burns, B.T., Cao, J., Cornilescu, C.C., Doreleijers, J.F., Ellefson, J.M., Frederick, R.O., Geetha, H.V., Hruby, D., Jeon, W.B., Johnson, K.A., Kimball, T.L., Kunert, J., Madson, S.E., Markley, J.L., Newman, C.S., Olson, A.C., Peterson, F.C., Phillips, G.N., Jr., Primm, J.G., Ramirez, B., Rosenberg, N.S., Runnels, M., Seder, K.D., Shaw, J., Smith, D.W., Sreenath, H.K., Song, J., Sussman, M., R., Thao, S., Troestler, D.M., Tyler, E.M., Tyler, R.C., Ulrich, E.L., Vinarov, D.A., Vojtik, F.C., Volkman, B.F., Wesenberg, G.E., Wrobel, R.L., Zhang, J., Zhao, Q., and Zolnai, Z. 2005 X-ray structure of Arabidopsis At1g77680, 12-oxophytodienolate reductase isoforms 1 Proteins61(1):206-8 X-ray Structural X 21K PMID:16080145
Frederick, R.O., Bergeman, L., Blommel, P.G., Bailey, L.J., McCoy, J.G., Song, J., Meske, L., Bingman, C.A., Riters, M., Dillon, N.A., Kunert, J., Yoon, J.W., Lim, A., Cassidy, M., Bunge, J., Aceti, D.J., Primm, J.G., Markley, J.L., Phillips, G.N., Jr., and Fox, B.G. 2007 Small-scale, semi-automated purification of eukaryotic proteins for structure determination JSFG 374(2):374-83 SSET Method X 232K PMID:17985212
Han, B.W., Bingman, C.A., Mahnke, D.K., Bannen, R.M., Bednarek, S., Sabina, R.L., and Phillips, G.N., Jr. 2006 Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1) J Biol Chem 281(21):14939-47 X-ray Structural X 231K PMID:16543243
Han, B.W., Bingman, C.A., Mahnke, D.K., Sabina, R.L., and Phillips, G.N., Jr. 2005 Crystallization and preliminary X-ray crystallographic analysis of adenosine 5'- monophosphate deaminase (AMPD) from Arabidopsis thaliana in complex with coformycin 5'-phosphate Acta Crystallograph Sect F Struct Biol Cryst Commun 61(Pt 8):740-2 X-ray Structural X 21K PMID:16511144
PMCID:PMC1952363
Han, B.W., Bingman, C.A., Wesenberg, G.E., and Phillips, G.N., Jr. 2006 Crystal structure of Homo sapiens thialysine Nepsilon-acetyltransferase (HsSSAT2) in complex with acetyl coenzyme A Proteins 64(1):288-93 X-ray Structural X 221K PMID:16596569
Hayes, P.L., Lytle, B.L., Volkman, B.F., and Peterson, F.C. 2008 The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominately unstructured protein Protein Sci 17(3):571-6 NMR Structural X 233K PMID:18287285
PMCID:PMC2248319
(on 03/01/09)
Hegeman, A.D., Rodriguez, M., Han, B.W., Uno, Y., Phillips, G.N., Jr., Hrabak, E.M., Cushman, J.C., Harper, J.F., Harmon, A.C., and Sussman, M.R. 2006 A phyloproteomic characterization of in vitro autophosphorylation in calcium dependent protein kinases Proteomics 6(12):3649-64 X-ray Method X 221K PMID:16758442
Jamrog, D.C., Phillips, G.N., Jr., Tapia, R., and Zhang, Y. 2005 A global optimization method for the molecular replacement problem in X-ray crystallography Mathematical Programming Series B X-ray Method X 1K
Jamrog, D.C., Zhang, Y., and Phillips, G.N., Jr. 2003 SOMoRe: a multi-dimensional search and optimization approach to molecular replacement Acta Crystallogr D Biol Crystallogr 59(Pt 2):304-14 X-ray Method X 1K PMID:12554941
Jamrog, D.C., Zhang, Y., and Phillips, G.N., Jr. 2004 On the equivalence between a commonly used correlation coefficient and a least-squares function Acta Crystallogr A 60(Pt 3):214-9 X-ray Method X 1K PMID:15103164
Jeon, W.B., Aceti, D.J., Bingman, C.A., Vojtik, F.C., Olson, A.C., Ellefson, J.M., McCombs, J.E., Sreenath, H.K., Blommel, P.G., Seder, K.D., Buchan, B.W., Burns, B.T., Geetha, H.V., Harms, A., Sabat, G., Sussman, M.R., Fox, B.G., and Phillips, G.N., Jr. 2005 High-throughput purification and quality assurance of Arabidopsis thaliana proteins for eukaryotic structural genomics JSFG 6:143-7 PP Method X 1K PMID:16211511
Jeon, W.B., Allard, S.T.M., Bingman, C.A., Bitto, E., Han, B.W., Wesenberg, G.E., and Phillips, G.N., Jr. 2006 X-ray crystal structures of the conserved hypothetical proteins from Arabidopsis thaliana gene loci At5g11950 and At2g37210 Proteins 65(4):1051-4 X-ray Structural X 221K PMID:17048257
Johnson, R.J., McCoy, J.G., Bingman, C.A., Phillips, G.N., Jr., and Raines, R.T. 2007 Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein J Mol Biol 368(2):434-49 X-ray Structural X 223K PMID:17350650
PMCID:PMC1993901
Kennedy, M.A., Montelione, G., Arrowsmith, C.H., and Markley, J.L. 2002 Role for NMR in structural genomics JSFG 2(3):155-69 NMR Method X 1K PMID:12836706
Kifer, I., Sasson, O., and Linial, M. 2005 Predicting fold novelty based on ProtoNet hierarchical classification Bioinformatics 21(7):1020-7 BI Method X 1K PMID:15539447
Kundu, S., Melton, J.S., Sorensen, D.C., and Phillips, G.N., Jr. 2002 Dynamics of proteins in crystals: comparison of experiment with simple models Biophys J 83(2):723-32 X-ray Method X 1K PMID:12124259
PMCID:PMC1302181
Kundu, S., Sorensen, D.C., and Phillips, G.N., Jr. 2004 Automatic domain decomposition of proteins by a Gaussian Network Model Proteins 57(4):725-33 BI Method X 1K PMID:15478120
Lee, J.E., Bae, E., Bingman, C.A., Phillips, G.N., Jr., and Raines, R.T. 2007 Structural basis for catalysis by onconase J Mol Biol 375(1):165-77 X-ray Structural X 222K PMID:18001769
PMCID:PMC2151974
(on 01/04/09)
Levin, E.J., Elsen, N.L., Seder, K.D., McCoy, J.G., Fox, B.G., Phillips, G.N., Jr. 2008 X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus Acta Crystallogr D Biol Crystallogr 64(Pt 9):933-40 X-ray Structural X 241 PMID:18703841
Levin, E.J., Kondrashov, D.A., Wesenberg, G.E., and Phillips, G.N., Jr. 2007 Ensemble refinement of protein crystal structures, validation, and application Structure 15(9):1040-52 X-ray Method X 231K PMID:17850744
PMCID:PMC2039884
(on 09/01/08)
Lytle, B.L., Peterson, F.C., Kjer, K.L., Frederick, R.O., Zhao, Q., Thao, S., Bingman, C.A., Johnson, K.A., Phillips, G.N., Jr., and Volkman, B.F. 2004 Structure of the hypothetical protein At3g17210 from Arabidopsis thaliana J Biomol NMR 28(4):397-400 NMR Structural X 1K PMID:14872131
Lytle, B.L., Peterson, F.C., Qiu, S.-H., Luo, M., Zhao, Q., Markley, J.L., and Volkman, B.F. 2004 Solution structure of a ubiquitin-like domain from tubulin-binding cofactor B J Biol Chem 279(45):46787-93 NMR Structural X 1K PMID:15364906
Lytle, B.L., Peterson, F.C., Tyler, E.M., Vinarov, D.A., Markley, J.L., and Volkman, B.F. 2006 Solution structure of Arabidopsis thaliana protein At5g39720.1, a member of the AIG2-like protein family Acta Crystallograph Sect F Struct Biol Cryst Commun 62(Pt 6):490-3 NMR Structural X 221K PMID:16754964
PMCID:MC2243094
Malone, T.E., Madson, S.E., Wrobel, R.L., Jeon, W.B., Rosenberg, N.S., Johnson, K.A., Bingman, C.A., Smith, D.W., Phillips, G.N., Jr., Markley, J.L., and Fox, B.G. 2004 X-ray structure of Arabidopsis At2g06050, 12-oxophytodienoate reductase isoform 3 Proteins 58(1):243-5 X-ray Structural X 1K PMID:15468319
Markley, J.L. 2007 NMR-Based Structural Proteomics Spectral Techniques in Proteomics, Blackwell Publishing, Taylor and Francis Ltd. 349-71 NMR Method X 224 Not Applicable
Markley, J.L., Ulrich, E.L., Westler, W.M., and Volkman, B.F. 2003 Macromolecular structure determination by NMR spectroscopy Methods of Biochemical Analysis, Wiley Publishers 44:89-113 NMR Method 1K PMID:12647383
McCoy, J.G., Arabshahi, A., Bitto, E., Bingman, C.A., Ruzicka, F.J., Frey, P.A., and Phillips, G.N., Jr. 2006 Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana Biochemistry 45(10):3154-62 X-ray Structural X 21K PMID:16519510
McCoy, J.G., Bailey, L.J., Bitto, E., Bingman, C.A., Aceti, D.J., Fox, B.G., and Phillips, G.N., Jr. 2006 Structure and mechanism of mouse cysteine dioxygenase Proc Natl Acad Sci USA 103(9):3084-9 X-ray Structural X 21K PMID:16492780
PMCID:PMC1413891
McCoy, J.G., Bailey, L.J., Bitto, E., Ng, L.J., Bingman, C.A., Wrobel, R.L.., Fox, B.G., and Phillips, G.N., Jr. 2008 Discovery of sarcosine dimethylglycine methyltransferase from Galderia sulphuraria Proteins (in press) X-ray Structural 234 PMID:18623062
McCoy, J.G., Bingman, C.A., Bitto, E., Holdorf, M.M., Makaroff, C.A., and Phillips, G.N., Jr. 2006 Structure of an ETHE1-like protein from Arabidopsis thaliana Acta Crystallogr D Biol Crystallogr 62(Pt 9):964-70 X-ray Structural X 21K PMID:16929096
McCoy, J.G., Bitto, E., Bingman, C.A., Wesenberg, G.E., Bannen, R.M., Kondrashov, D.A., and Phillips, G.N., Jr. 2006 Structure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP J Mol Biol 366(3):830-41 X-ray Structural X 221K PMID:17178129
PMCID:PMC1847403
McCoy, J.M., Johnson, H., Singh, S., Bingman, C.A., Lei, I-K., Thorson, J., and Phillips, G.N., Jr. 2008 Structural characterization of CalO2: a putative orsellinic acid P450 oxidase in the calicheamicin biosynthetic pathway Proteins (in press) X-ray Structural 234K PMID:18561189
Moe, L.A., Bingman, C.A., Wesenberg, G.E., Phillips, G.N., Jr., and Fox, B.G. 2006 Structure of T4moC, the Rieske-type ferredoxin component of toluene 4-monooxygenase Acta Crystallogr D Biol Crystallogr 62(Pt 5):476-82 X-ray Structural X 21K PMID:16627939
Nederveen, A.J., Doreleijers, J.F., Vranken, W., Miller, Z., Spronk, C.A.E.M., Nabuurs, S.B., Guntert, P., Livny, M., Markley, J.L., Nilges, M., Ulrich, E.L., Kaptein, R., and Bonvin, A.M.J.J. 2005 RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank Proteins 59(4):662-72 BI Method X 1K PMID:15822098
Oldfield, C.J., Ulrich, E.L., Cheng, Y.G., Dunker, A.K., and Markley, J.L. 2004 Addressing the intrinsic disorder bottleneck in structural proteomics Proteins 59(3):444-53 BI Method X 1K PMID:15789434
Pan, X., Wesenberg, G.E., Markley, J.L., Fox, B.G., Phillips, G.N., Jr., and Bingman, C.A. 2008 A graphical approach to tracking and reporting target status in structural genomics JSFG 8(4):209-16 BI Method X 233K PMID:18236171
Peterson, F.C., Hayes, P.L., Waltner, J.K., Heisner, A.K., Jensen, D.R., Sander, T.L., and Volkman, B.F. 2006 Structure of the SCAN domain from the tumor suppressor protein MZF1 J Mol Biol 363(1):137-47 NMR Structural X 21K PMID:16950398
PMCID:PMC1941711
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PMCID:PMC2279331
Phillips, G.N., Jr., Fox, B.G., Markley, J.L., Volkman, B.F., Bae, E., Bitto, E., Bingman, C.A., Frederick, R.O., McCoy, J.G., Lytle, B.L., Pierce, B.S., Song, J., and Twigger, S.N. 2007 Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics JSFG 8(2-3):73-84 All Structural X 231K PMID:17786587
Rayment, I. 2002 Small-scale batch crystallization of proteins revisited: an underutilized way to grow large protein crystals Structure 10(2):147-51 X-ray Method X 1K PMID:11839300
Sabina, R.L., Paul, A.L., Ferl, R.J., Laber, B., and Lindell, S.D. 2007 Adenine nucleotide pool perturbation is a metabolic trigger for AMP deaminase inhibitor-based herbicide toxicity Plant Physiol 143(4):1752-60 None Method X 224K PMID:17307896
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Sasson, O., and Linial, M. 2005 Predicting fold novelty based on ProtoNet hierarchical classification Bioinformatics 21(7):1020-7 BI Method X 21K PMID:15539447
Singh, S., Cornilescu, C.C., Tyler, R.C., Cornilescu, G., Tonelli, M., Lee, M.S., and Markley, J.L. 2005 Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related protein Protein Sci 14(10):2601-9 NMR Structural X 21K PMID:16155204
PMCID:PMC2253292
Singh, S., McCoy, J.G., Zhang, C., Bingman, C.A., Phillips, G.N., Jr., Thorson, J.S. 2008 Structure and mechanism of the rebeccamycin sugar 4'-O-methyltransferase RebM J Biol Chem 283(33):22628-36 NMR Structural X 234K PMID:18502766
Singh, S., Hager, M.H., Zhang, C., Griffith, B.R., Lee, M.S., Hallenga, K., Markley, J.L., and Thorson, J.S. 2006 Structural insight into the self-sacrifice mechanism of enediyne resistance ACS Chem Biol 1(7):451-60 NMR Structural X 221K PMID:17168523
Singh, S., Tonelli, M., Tyler, R.C., Bahrami, A., Lee, M.S., and Markley, J.L. 2005 Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1 Protein Sci 14(8):2095-102 NMR Structural X 1K PMID:16046629
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Skjeldal, L., Peterson, F.C., Moe, L.A., Pikus, J.D., Doreleijers, J.F., Volkman, B.F., Westler, W.M., Markley, J.L., and Fox, B.G. 2004 Solution structure of T4moC, the Rieske ferredoxin component of the toluene 4-monooxygenase complex J Inorg Biol Chem 9(8):945-53 NMR Structural X 1K PMID:15452777
Smith, D.W., Johnson, K.A., Bingman, C.A., Aceti, D.J., Blommel, P.G., Wrobel, R.L., Frederick, R.O., Zhao, Q., Sreenath, H.K., Fox, B.G., Volkman, B.F., Jeon, W.B., Newman, C.S., Ulrich, E.L., Hegeman, A.D., Kimball, T.L., Thao, S., Sussman, M.R., Markley, J.L., and Phillips, G.N., Jr. 2004 Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thaliana Proteins 57(4):854-7 X-ray Structural X 1K PMID:15317023
Sobrado, P., Goren, M.A., James, D., Amundson, C.K., and Fox, B.G. 2008 A Protein Structure Initiative approach to expression, purification, and in situ delivery of human cytochrome b5 to membrane vesicles. Protein Expr Purif 58(2):229-41 Cloning Method X PMID:18226920
PMCID:PMC2277500
(on 04/01/09)
Song, J., Bettendorff, L., Tonelli, M., and Markley, J.L. 2008 Structural basis for the catalytic mechanism of mammalian 25 kDa thiamine triphosphatase J Biol Chem 283(16):10939-48 NMR Structural X 233K PMID:18276586
PMCID:PMC2447667
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PMCID:PMC2234174
Song, J., Lee, M.S., Carlberg, I., Vener, A.V., and Markley, J.L. 2006 Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications Biochemistry 45(51):15633-43 NMR Structural X 221K PMID:17176085
PMCID:in progress
Song, J., and Markley, J.L. 2007 Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold J Mol Biol 366(1):155-64 NMR Structural X 222K PMID:17166513
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Song, J., and Markley, J.L. 2007 Cautionary tail: the presence of an N-terminal tag on dynein light-chain Roadblock/LC7 affects its interaction with a functional partner Protein Pept Lett 14(3):265-8 NMR Structural X 222K PMID:17346231
Song, J., Tyler, R.C., Lee, M.S., Tyler, E.M., and Markley, J.L. 2005 Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complex J Mol Biol 354(5):1043-51 NMR Structural X 21K PMID:16289575
Song, J., Tyler, R.C., Wrobel, R.L., Frederick, R.O., Vojtik, F.C., Jeon, W.B., Lee, M.S., and Markley, J.L. 2005 Solution structure of At3g04780.1-des15, an Arabidopsis thaliana ortholog of the C-terminal domain of human thioredoxin-like protein Protein Sci 14(4):1059-63 NMR Structural X 1K PMID:15741346
PMCID:PMC2253455
Song, J., Vinarov, D.A., Tyler, E.M., Shahan, M.N., Tyler, R.C., and Markley, J.L. 2004 Hypothetical protein At2g24940.1 from Arabidopsis thaliana has a cytochrome B5 like fold J Biomol NMR 30(2):215-8 NMR Structural X 1K PMID:15702529
Song, J., Zhao, K.Q., Newman, C.L., Vinarov, D.A., and Markley, J.L. 2007 Solution structure of human sorting nexin 22 Protein Sci 16(5):807-14 NMR Structural X 224K PMID:17400918
PMCID:PMC2206652
Song, J., Zhao, Q., Lee, M.S., and Markley, J.L. 2005 1H, 15N, and 13C resonance assignments of the putative Bet v 1 family protein At1g24000.1 from Arabidopsis thaliana J Biomol NMR 32(4):335 NMR Structural X 21K PMID:16211487
Song, J., Zhao, Q., Thao, S., Frederick, R.O., and Markley, J.L. 2004 Solution structure of a calmodulin-like calcium-binding domain from Arabidopsis thaliana J Biomol NMR 30(4):451-6 NMR Structural X 1K PMID:15630565
Sreenath, H.K., Bingman, C.A., Buchan, B.W., Seder, K.D., Burns, B.T., Geetha, H.V., Jeon, W.B., Vojtik, F.C., Aceti, D.J., Frederick, R.O., Phillips, G.N., Jr., and Fox, B.G. 2005 Protocols for production of selenomethionine-labeled proteins in 2-L polyethylene terephthalate bottles using auto-induction medium Prot Expr Purif 40(2):256-67 PP Method X 1K PMID:15766867
Stolc, V., Samanta, M.P., Tongprasit, W., Sethi, H., Liang, S., Hegeman, A.D., Nelson, C., Rancou, D., Bednarek, S., Ulrich, E.L., Zhao, Q., Wrobel, R.L., Newman, C.S., Fox, B.G., Phillips, G.N., Jr., Markley, J.L., and Sussman, M.R. 2005 Identification of transcribed sequences in Arabidopsis thaliana using high-resolution genome tiling arrays Proc Natl Acad Sci USA 102(12):4453-8 Cloning Method X 1K PMID:15755812
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Sugimori, N., Torizawa, T., Aceti, D.J., Thao, S., Markley, J.L., and Kainosho, M. 2004 1H, 13C, and 15N backbone assignment of a 32 kDa hypothetical protein from Arabidopsis thaliana At3g16450.1 J Biomol NMR 30(3):357-8 NMR Structural X 1K PMID:15756462
Thao, S., Zhao, Q., Kimball, T., Steffen, E., Blommel, P.G., Riters, M., Newman, C.S., Fox, B.G., and Wrobel, R.L. 2004 Results from high-throughput DNA cloning of Arabidopsis thaliana target genes using site-specific recombination JSFG 5(4):267-76 Cloning Method X 1K PMID:15750721
Torizawa, T., Shimizua, M., Taoka, M., Miyano, H., and Kainosho, M. 2004 Efficient production of isotopically labeled proteins by cell-free synthesis: a practical protocol J Biomol NMR 30(3):311-25 Cell-Free Method X 1K PMID:15754057
Tyler, R.C., Aceti, D.J., Bingman, C.A., Cornilescu, C.C., Fox, B.G., Frederick, R.O., Jeon, W.B., Lee, M.S., Newman, C.S., Peterson, F.C., Phillips, G.N., Jr., Shahan, M.N., Singh, S., Song, J., Sreenath, H.K., Tyler, E.M., Ulrich, E.L., Vinarov, D.A., Vojtik, F.C., Volkman, B.F., Wrobel, R.L., Zhao, Q., and Markley, J.L. 2005 Comparison of cell-based and cell-free protocols for producing target proteins from Arabidopsis thaliana for structural studies Proteins 59(3):633-43 NMR Method X 1K PMID:15789406
Tyler, R.C., Bitto, E., Berndsen, C.E., Bingman, C.A., Singh, S., Lee, M.S., Wesenberg, G.E., Denu, J.M., Phillips, G.N., Jr., and Markley, J.L. 2006 Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family Biochemistry 45(48):14325-36 X-ray Structural X 221K PMID:17128971
Tyler, R.C., Sreenath, H.K., Aceti, D.J., Bingman, C.A., Singh, S., Markley, J.L., and Fox, B.G. 2004 Auto-induction medium for the production of [U-15N] and [U-13C, U-15N]-labeled proteins for NMR screening and structure determination Prot Expr Purif 40(2):268-78 NMR Method X 1K

PMID:15766868

Vinarov, D.A., Lytle, B.L., Peterson, F.C., Tyler, E.M., Volkman, B.F., and Markley, J.L. 2004 Cell-free protein production and labeling protocol for NMR-based structural proteomics Nat Methods 1(2):149-53 Cell-Free Method X 1K PMID:15782178
Vinarov, D.A., and Markley, J.L. 2005 High-throughput automated platform for nuclear magnetic resonance-based structural proteomics Expert Rev Proteomics 2(1):49-55 Cell-Free Method X 1K PMID:15966852
Vinarov, D.A., Newman, C.L., and Markley, J.L. 2006 Wheat germ cell-free platform for eukaryotic protein production FEBS J 273(18):4160-9 Cell-Free Method X 222K PMID:16930128
Vinarov, D.A., Newman, C.L., Tyler, E.M., Markley, J.L., and Shahan, M.N. 2006 Wheat germ cell-free expression system for protein production Current Protocols in Protein Science, Wiley Interscience Cell-Free Method X 231K Not Applicable
Waltner, J.K., Lytle, B.L., Sampath, S., Vinarov, D.A., Tyler, E.M., Shahan, M.N., Markley, J.L., and Volkman, B.F. 2005 Structure of the B3 domain from Arabidopsis thaliana protein At1g16640 Protein Sci 14(9):2478-83 NMR Structural X 1K PMID:16081658
PMCID:PMC2253459
Wang, L., Eghbalnia, H.R., Bahrami, A., and Markley, J.L. 2005 Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications J Biomol NMR 32(1):13-22 NMR Method X 1K PMID:16041479
Wang, L., Eghbalnia, H.R., and Markley, J.L. 2006 Probabilistic approach to determining unbiased random-coil carbon-13 chemical shift values from the protein chemical shift database J Biomol NMR 35(3):155-65 NMR Method X 21K PMID:16799859
Wang, L., Eghbalnia, H.R., and Markley, J.L. 2007 Nearest-neighbor effects on backbone alpha and beta carbon chemical shifts in proteins J Biomol NMR 39(3):247-57 NMRMethod X 231K PMID:17899393
Wrobel, R.L., Bingman, C.A., Jeon, W.B., Song, J., Vinarov, D.A., Frederick, R.O., Aceti, D.J., Sreenath, H.K., Zolnai, Z., Vojtik, F.C., Bitto, E., Fox, B.G., Phillips, G.N., Jr., and Markley, J.L. 2006 Structural Proteomics Plant Proteomics, Blackwell Publishing 99-128 Cloning Method 21 Not Applicable
Zhao, Q., Chae, Y.K., and Markley, J.L. 2002 NMR solution structure of ATTp, an Arabidopsis thaliana trypsin inhibitor Biochemistry 41:12284-96 NMR Structural X 1K PMID:12369816
Zhang, C., Bitto, E., Goff, R.D., Singh, S., Bingman, C.A., Griffith, B.R., Alberman, C,. Phillips, G.N., Jr., and Thomas, J.S. 2008 Biochemical and structural insights of the early glycosylation steps in calcicheamicin biosnythesis Chem and Bio (in press) X-ray Structural 234
Zhao, Q., Frederick, R.O., Seder, K.D., Thao, S., Sreenath, H.K., Peterson, F.C., Volkman, B.F., Markley, J.L., and Fox, B.G. 2004 Production in two-liter beverage bottles of proteins for NMR structure determination labeled with either 15N- or 13C;15N JSFG 5(1-2):87-93 NMR Method X 1K