Items where Subject is "protein structure rendering"

Paper

Ahmed, Shehab S, Rifat, Zaara T, Lohia, Ruchi, Campbell, Arthur J, Dunker, A Keith, Rahman, M Sohel, Iqbal, Sumaiya (March 2022) Characterization of intrinsically disordered regions in proteins informed by human genetic diversity. PLoS Computational Biology, 18 (3). e1009911. ISSN 1553-734X

Auster, A. S., Joshua-Tor, L. (January 2004) The DNA-binding domain of human papillomavirus type 18 E1. Crystal structure, dimerization, and DNA binding. J Biol Chem, 279 (5). pp. 3733-42. ISSN 0021-9258 (Print) (Public Dataset)

Barford, D., Jia, Z. C., Tonks, N. K. (December 1995) Protein tyrosine phosphatases take off. Nature Structural Biology, 2 (12). pp. 1043-1053. ISSN 1072-8368

Bhattacharya, Nicholas, Thomas, Neil, Rao, Roshan, Dauparas, Justas, Koo, Peter K, Baker, David, Song, Yun S, Ovchinnikov, Sergey (2022) Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 27. pp. 34-45. ISSN 2335-6936

Brinda, K. V., Kannan, N., Vishveshwara, S. (April 2002) Analysis of homodimeric protein interfaces by graph-spectral methods. Protein Engineering, 15 (4). pp. 265-277. ISSN 0269-2139

Cai, L., Harris, W. R., Marshak, D. R., Gross, J., Crabb, J. W. (October 1990) Structural analysis of bovine pancreatic thread protein. J Protein Chem, 9 (5). pp. 623-32. ISSN 0277-8033 (Print)0277-8033 (Linking)

Chardin, P., Camonis, J. H., Gale, N. W., van Aelst, L., Schlessinger, J., Wigler, M. H., Bar-Sagi, D. (May 1993) Human Sos1: a guanine nucleotide exchange factor for Ras that binds to GRB2. Science, 260 (5112). pp. 1338-1343.

David, S. S., Golinelli, M. P., Chmiel, N. H., Langer, M. R., Chepanoske, C. L., Messick, T. R., Joshua-Tor, L. (August 2001) Participation of the iron-sulfur cluster loop (FCL) motif of the adenine glycosylase MutY in DNA damage recognition and repair. Abstracts of Papers of the American Chemical Society, 222. U578-U578. ISSN 0065-7727

Day, M. W., Hsu, B. T., Joshua-Tor, L., Park, J. B., Zhou, Z. H., Adams, M. W. W., Rees, D. C. (1992) X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Science, 1 (11). pp. 1494-1507. ISSN 09618368 (ISSN) (Public Dataset)

Elegheert, Jonathan, Cvetkovska, Vedrana, Clayton, Amber J, Heroven, Christina, Vennekens, Kristel M, Smukowski, Samuel N, Regan, Michael C, Jia, Wanyi, Smith, Alexandra C, Furukawa, Hiro, Savas, Jeffrey N, de Wit, Joris, Begbie, Jo, Craig, Ann Marie, Aricescu, A Radu (September 2017) Structural Mechanism for Modulation of Synaptic Neuroligin-Neurexin Signaling by MDGA Proteins. Neuron, 96 (1). pp. 242-244. ISSN 0896-6273

Enemark, E. J., Stenlund, A., Joshua-Tor, L. (March 2002) Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex. Embo Journal, 21 (6). pp. 1487-1496. ISSN 0261-4189 (Public Dataset)

Gerst, J. E., Field, J., Ferguson, K., Wigler, M. H. (1990) Molecular and Phenotypic Analysis of Cap a Regulatory Element Involved in Mediating Both Ras Action and Amino Acid Balance. Yeast, 6 (SPEC. ). S174.

Gerst, J. E., Rodgers, L., Riggs, M., Wigler, M. (May 1992) SNC1, a yeast homolog of the synaptic vesicle-associated membrane protein/synaptobrevin gene family: genetic interactions with the RAS and CAP genes. Proc Natl Acad Sci U S A, 89 (10). pp. 4338-42. ISSN 0027-8424 (Print)0027-8424 (Linking)

Hansen, K. B., Furukawa, H., Traynelis, S. F. (October 2010) Control of Assembly and Function of Glutamate Receptors by the Amino-Terminal Domain. Molecular Pharmacology, 78 (4). pp. 535-549. ISSN 0026-895X

Huang, Z. J., Curtin, K. D., Rosbash, M. (1995) PER protein interactions and temperature compensation of a circadian clock in Drosophila. Science, 267 (5201). pp. 1169-1172. ISSN 00368075 (ISSN)

Jaremko, M. J., On, K. F., Thomas, D. R., Stillman, B., Joshua-Tor, L. (August 2020) The dynamic nature of the human origin recognition complex revealed through five cryoEM structures. Elife, 9. e58622. ISSN 2050-084x

Jia, Z. C., Barford, D., Flint, A. J., Tonks, N. K. (June 1995) Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B. Science, 268 (5218). pp. 1754-1758. ISSN 0036-8075

Jin, R., Singh, S. K., Gu, S., Furukawa, H., Sobolevsky, A. I., Zhou, J., Jin, Y., Gouaux, E. (June 2009) Crystal structure and association behaviour of the GluR2 amino-terminal domain. Embo J, 28 (12). pp. 1812-23. ISSN 1460-2075 (Electronic)1460-2075 (Linking) (Public Dataset)

Johnson, K. E., Cameron, S., Toda, T., Wigler, M. H., Zoller, M. J. (1987) Expression in Escherichia coli of BCY1, the regulatory subunit of cyclic AMP-dependent protein kinase from Saccharomyces cerevisiae. Journal of Biological Chemistry, 262 (18). pp. 8636-8642.

Karakas, E., Simorowski, N., Furukawa, H. (November 2009) Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit. Embo Journal, 28 (24). pp. 3910-3920. ISSN 0261-4189 (Public Dataset)

Kataoka, T., Broek, D., Wigler, M. H. (December 1985) DNA sequence and characterization of the S. cerevisiae gene encoding adenylate cyclase. Cell, 43 (2). pp. 493-505. ISSN 0092-8674

Kawamukai, M., Gerst, J., Field, J., Riggs, M., Rodgers, L., Wigler, M. H., Young, D. (February 1992) Genetic and biochemical analysis of the adenylyl cyclase-associated protein, cap, in Schizosaccharomyces pombe. Molecular Biology of the Cell, 3 (2). pp. 167-180. ISSN 1059-1524

Kumar, P. R., Yu, Y., Sternglanz, R., Johnston, S. A., Joshua-Tor, L. (February 2008) NADP regulates the yeast GAL induction system. Science, 319 (5866). pp. 1090-2. ISSN 1095-9203 (Electronic) (Public Dataset)

Lavy, T., Kumar, P. R., He, H. Z., Joshua-Tor, L. (February 2012) The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation. Genes & Development, 26 (3). pp. 294-303. ISSN 0890-9369 (Public Dataset)

Levin, L. R., Kuret, J., Johnson, K. E., Powers, S., Cameron, S., Michaeli, T., Wigler, M. H., Zoller, M. J. (April 1988) A mutation in the catalytic subunit of cAMP-dependent protein kinase that disrupts regulation. Science, 240 (4848). pp. 68-70.

Messick, T. E., Chmiel, N. H., Golinelli, M. P., Langer, M. R., Joshua-Tor, L., David, S. S. (March 2002) Noncysteinyl coordination to the [4Fe-4S](2+) cluster of the DNA repair adenine glycosylase MutY introduced via site-directed mutagenesis. Structural characterization of an unusual histidinyl-coordinated cluster. Biochemistry, 41 (12). pp. 3931-3942. ISSN 0006-2960 (Public Dataset)

Min, J. R., Landry, J., Sternglanz, R., Xu, R. M. (April 2001) Crystal structure of a SIR2 homolog-NAD complex. Cell, 105 (2). pp. 269-279. ISSN 0092-8674

O'Farrell, P. A., Gonzalez, F., Zheng, W., Johnston, S. A., Joshua-Tor, L. (June 1999) Crystal structure of human bleomycin hydrolase, a self-compartmentalizing cysteine protease. Structure, 7 (6). pp. 619-27. ISSN 0969-2126 (Public Dataset)

Pavlovsky, A. G., Liu, X., Faehnle, C. R., Potente, N., Viola, R. E. (January 2012) Structural characterization of inhibitors with selectivity against members of a homologous enzyme family. Chemical Biology and Drug Design, 79 (1). pp. 128-136. ISSN 17470277 (ISSN)

Russell, S. J., Gonzalez, F., Joshua-Tor, L., Johnston, S. A. (October 2001) Selective chemical inactivation of AAA proteins reveals distinct functions of proteasomal ATPases. Chemistry & Biology, 8 (10). pp. 941-950. ISSN 1074-5521

Schalch, T., Job, G., Shanker, S., Partridge, J. F., Joshua-Tor, L. (2011) The Chp1-Tas3 core is a multifunctional platform critical for gene silencing by RITS. Nature Structural and Molecular Biology, 18 (12). pp. 1351-1357. ISSN 15459993 (ISSN) (Public Dataset)

Schlessman, J. L., Woo, D., Joshua-Tor, L., Howard, J. B., Rees, D. C. (1998) Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum. Journal of Molecular Biology, 280 (4). pp. 669-685. ISSN 00222836 (ISSN) (Public Dataset)

Short, M. N., Turner, D. S., March, J. F., Pappin, D. J., Parente, A., Davies, J. W. (July 1986) The primary structure of papaya mosaic virus coat protein. Virology, 152 (1). pp. 280-3. ISSN 0042-6822 (Print)0042-6822 (Linking)

Syrjanen, J. L., Michalski, K., Chou, T. H., Grant, T., Rao, S., Simorowski, N., Tucker, S. J., Grigorieff, N., Furukawa, H. (January 2020) Structure and assembly of calcium homeostasis modulator proteins. Nat Struct Mol Biol, 27 (2). pp. 150-159. ISSN 1545-9985 (Public Dataset)

Syrjanen, Johanna L, Michalski, Kevin, Chou, Tsung-Han, Grant, Timothy, Rao, Shanlin, Simorowski, Noriko, Tucker, Stephen J, Grigorieff, Nikolaus, Furukawa, Hiro (March 2020) Publisher Correction: Structure and assembly of calcium homeostasis modulator proteins. Nature Structural and Molecular Biology, 27 (3). p. 305. ISSN 1545-9993

Takahashi, H., Shin, Y., Cho, S. J., Zago, W. M., Nakamura, T., Gu, Z., Ma, Y., Furukawa, H., Liddington, R., Zhang, D., Tong, G., Chen, H. S., Lipton, S. A. (January 2007) Hypoxia enhances S-nitrosylation-mediated NMDA receptor inhibition via a thiol oxygen sensor motif. Neuron, 53 (1). pp. 53-64. ISSN 0896-6273 (Print)0896-6273 (Linking)

Turner, G. C., Varshavsky, A. (2000) Detecting and measuring cotranslational protein degradation in vivo. Science, 289 (5487). pp. 2117-2120. ISSN 00368075 (ISSN)

Van Aalten, D. M. F., Crielaard, W., Hellingwerf, K. J., Joshua-Tor, L. (January 2000) Conformational substates in different crystal forms of the photoactive yellow protein - Correlation with theoretical and experimental flexibility. Protein Science, 9 (1). pp. 64-72. ISSN 0961-8368 (Public Dataset)

Van Aalten, D. M. F., Crielaard, W., Hellingwerf, K. J., Joshua-Tor, L. (2002) Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 Å resolution. Acta Crystallographica Section D: Biological Crystallography, 58 (4). pp. 585-590. ISSN 09074449 (ISSN) (Public Dataset)

Van Aalten, D. M. F., Grotewold, E., Joshua-Tor, L. (March 1998) Essential dynamics from NMR clusters: Dynamic properties of the Myb DNA-binding domain and a hinge-bending enhancing variant. Methods, 14 (3). pp. 318-328. ISSN 10462023 (ISSN)

Vasquez, V., Cortes, D. M., Furukawa, H., Perozo, E. (June 2007) An optimized purification and reconstitution method for the MscS channel: strategies for spectroscopical analysis. Biochemistry, 46 (23). pp. 6766-73. ISSN 0006-2960 (Print)0006-2960 (Linking)

Vaughn, D. E., Rodriguez, J., Lazebnik, Y., Joshua-Tor, L. (1999) Crystal structure of Apaf-1 caspase recruitment domain: an alpha-helical Greek key fold for apoptotic signaling. Journal of Molecular Biology, 293 (3). pp. 439-447. ISSN 0022-2836 (Public Dataset)

Wilbur, W. J., Neuwald, A. F. (January 2000) A theory of information with special application to search problems. Computers & Chemistry, 24 (1). pp. 33-42. ISSN 0097-8485

Yang, Z., Xue, B., Umitsu, M., Ikura, M., Muthuswamy, S. K., Neel, B. G. (August 2012) The Signaling Adaptor Gab1 Regulates Cell Polarity by Acting as a PAR Protein Scaffold. Molecular Cell, 47 (3). pp. 469-483.

Yasunaga, Mai, Ipsaro, Jonathan J., Mondragón, Alfonso (April 2012) Structurally Similar but Functionally Diverse ZU5 Domains in Human Erythrocyte Ankyrin. Journal of Molecular Biology, 417 (4). pp. 336-350. ISSN 0022-2836

Young, D., O'Neill, K., Broek, D., Wigler, M. H. (June 1991) The adenylyl cyclase-encoding gene from Saccharomyces kluyveri. Gene, 102 (1). pp. 129-32. ISSN 0378-1119

Young, D., Riggs, M., Field, J., Vojtek, A., Broek, D., Wigler, M. H. (October 1989) The adenylyl cyclase gene from Schizosaccharomyces pombe. Proc Natl Acad Sci U S A, 86 (20). pp. 7989-93. ISSN 0027-8424

Young, D., Waitches, G., Birchmeier, C., Fasano, O., Wigler, M. H. (1986) Isolation and characterization of a new cellular oncogene encoding a protein with multiple potential transmembrane domains. Cell, 45 (5). pp. 711-720.

Zheng, W., Johnston, S. A., Joshua-Tor, L. (April 1998) The unusual active site of Gal6/bleomycin hydrolase can act as a carboxypeptidase, aminopeptidase, and peptide ligase. Cell, 93 (1). pp. 103-9. ISSN 0092-8674 (Print)0092-8674 (Linking) (Public Dataset)

van Aalten, D. M., Haker, A., Hendriks, J., Hellingwerf, K. J., Joshua-Tor, L., Crielaard, W. (February 2002) Engineering photocycle dynamics. Crystal structures and kinetics of three photoactive yellow protein hinge-bending mutants. J Biol Chem, 277 (8). pp. 6463-8. ISSN 0021-9258 (Print) (Public Dataset)

van Aalten, D. M. F., Chong, C. R., Joshua-Tor, L. (August 2000) Crystal structure of carboxypeptidase A complexed with D-cysteine at 1.75 A - inhibitor-induced conformational changes. Biochemistry, 39 (33). pp. 10082-10089. ISSN 0006-2960 (Public Dataset)

Book Section

Rees, D. C., Kim, J., Georgiadis, M. M., Komiya, H., Chirino, A. J., Woo, D., Schlessman, J., Chan, M. K., Joshua-Tor, L., Santillan, G., Chakrabarti, P., Hsu, B. T. (1993) Crystal Structures of the Iron Protein and Molybdenum-Iron Protein of Nitrogenase. In: Molybdenum Enzymes, Cofactors, and Model Systems. ACS Symposium Series, 535 (535). American Chemical Society, pp. 170-185. ISBN 0-8412-2708-X

Conference or Workshop Item

Furukawa, H (August 2017) Structure and pharmacology of NMDA receptors. In: ISN-ESN Meeting.