Garib Novruz Murshudov

Search results

• 2024

  Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

  Lawson, C. L., Kryshtafovych, A., Pintilie, G. D., Burley, S. K., Černý, J., Chen, V. B., Emsley, P., Gobbi, A., Joachimiak, A., Noreng, S., Prisant, M. G., Read, R. J., Richardson, J. S., Rohou, A. L., Schneider, B., Sellers, B. D., Shao, C., Sourial, E., Williams, C. I. & Williams, C. J. & 61 others, Yang, Y., Abbaraju, V., Afonine, P. V., Baker, M. L., Bond, P. S., Blundell, T. L., Burnley, T., Campbell, A., Cao, R., Cheng, J., Chojnowski, G., Cowtan, K. D., DiMaio, F., Esmaeeli, R., Giri, N., Grubmüller, H., Hoh, S. W., Hou, J., Hryc, C. F., Hunte, C., Igaev, M., Joseph, A. P., Kao, W. C., Kihara, D., Kumar, D., Lang, L., Lin, S., Maddhuri Venkata Subramaniya, S. R., Mittal, S., Mondal, A., Moriarty, N. W., Muenks, A., Murshudov, G. N., Nicholls, R. A., Olek, M., Palmer, C. M., Perez, A., Pohjolainen, E., Pothula, K. R., Rowley, C. N., Sarkar, D., Schäfer, L. U., Schlicksup, C. J., Schröder, G. F., Shekhar, M., Si, D., Singharoy, A., Sobolev, O. V., Terashi, G., Vaiana, A. C., Vedithi, S. C., Verburgt, J., Wang, X., Warshamanage, R., Winn, M. D., Weyand, S., Yamashita, K., Zhao, M., Schmid, M. F., Berman, H. M. & Chiu, W., 1 Jul 2024, In: Nature Methods. 21, 7, p. 1340-1348 9 p.

  Research output: Contribution to journal › Article › peer-review

• Post-translational modifications in the Protein Data Bank

  Schofield, L. C., Dialpuri, J. S., Murshudov, G. N. & Agirre, J., 1 Sept 2024, In: Acta crystallographica. Section D, Structural biology. 80, Pt 9, p. 647-660 14 p., D80.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
• 2023

  The CCP4 suite: integrative software for macromolecular crystallography

  Agirre, J., Atanasova, M., Bagdonas, H., Ballard, C. B., Baslé, A., Beilsten-Edmands, J., Borges, R. J., Brown, D. G., Burgos-Mármol, J. J., Berrisford, J. M., Bond, P. S., Caballero, I., Catapano, L., Chojnowski, G., Cook, A. G., Cowtan, K. D., Croll, T. I., Debreczeni, J. É., Devenish, N. E. & Dodson, E. J. & 74 others, Drevon, T. R., Emsley, P., Evans, G., Evans, P. R., Fando, M., Foadi, J., Fuentes-Montero, L., Garman, E. F., Gerstel, M., Gildea, R. J., Hatti, K., Hekkelman, M. L., Heuser, P., Hoh, S. W., Hough, M. A., Jenkins, H. T., Jiménez, E., Joosten, R. P., Keegan, R. M., Keep, N., Krissinel, E. B., Kolenko, P., Kovalevskiy, O., Lamzin, V. S., Lawson, D. M., Lebedev, A. A., Leslie, A. G. W., Lohkamp, B., Long, F., Malý, M., McCoy, A. J., McNicholas, S. J., Medina, A., Millán, C., Murray, J. W., Murshudov, G. N., Nicholls, R. A., Noble, M. E. M., Oeffner, R., Pannu, N. S., Parkhurst, J. M., Pearce, N., Pereira, J., Perrakis, A., Powell, H. R., Read, R. J., Rigden, D. J., Rochira, W., Sammito, M., Sánchez Rodríguez, F., Sheldrick, G. M., Shelley, K. L., Simkovic, F., Simpkin, A. J., Skubak, P., Sobolev, E., Steiner, R. A., Stevenson, K., Tews, I., Thomas, J. M. H., Thorn, A., Valls, J. T., Uski, V., Usón, I., Vagin, A., Velankar, S., Vollmar, M., Walden, H., Waterman, D., Wilson, K. S., Winn, M. D., Winter, G., Wojdyr, M. & Yamashita, K., 1 Jun 2023, In: Acta crystallographica. Section D, Structural biology. 79, Pt 6, p. 449-461 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2011

  Overview of the CCP4 suite and current developments

  Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A. & Wilson, K. S., Apr 2011, In: Acta Crystallographica. Section D, Biological Crystallography. 67, 4, p. 235-242 8 p.

  Research output: Contribution to journal › Article › peer-review

• REFMAC5 for the refinement of macromolecular crystal structures

  Murshudov, G. N., Skubak, P., Lebedev, A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vaguin, A. A., Apr 2011, In: Acta Crystallographica. Section D, Biological Crystallography. 67, p. 355-367 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2009

  "Conditional Restraints": Restraining the Free Atoms in ARP/wARP

  Mooij, W. T. M., Cohen, S. X., Joosten, K., Murshudov, G. N. & Perrakis, A., 13 Feb 2009, In: Structure. 17, 2, p. 183-189 7 p.

  Research output: Contribution to journal › Article › peer-review
• 2008

  ARP/wARP and molecular replacement: the next generation

  Cohen, S. X., Ben Jelloul, M., Long, F., Vagin, A., Knipscheer, P., Lebbink, J., Sixma, T. K., Lamzin, V. S., Murshudov, G. N. & Perrakis, A., 4 Jan 2008, In: Acta crystallographica section d-Biological crystallography. 64, 1, p. 49-60 12 p.

  Research output: Contribution to journal › Article › peer-review

• BALBES: a molecular-replacement pipeline

  Long, F., Vagin, A. A., Young, P. & Murshudov, G. N., 4 Jan 2008, In: Acta crystallographica section d-Biological crystallography. 64, 1, p. 125-132 8 p.

  Research output: Contribution to journal › Article › peer-review

• Model preparation in MOLREP and examples of model improvement using X-ray data

  Lebedev, A. A., Vagin, A. A. & Murshudov, G. N., 4 Jan 2008, In: Acta crystallographica section d-Biological crystallography. 64, 1, p. 33-39 7 p.

  Research output: Contribution to journal › Article › peer-review

• Surprises and pitfalls arising from (pseudo)symmetry

  Zwart, P. H., Grosse-Kunstleve, R. W., Lebedev, A. A., Murshudov, G. N. & Adams, P. D., 4 Jan 2008, In: Acta crystallographica section d-Biological crystallography. 64, 1, p. 99-107 9 p.

  Research output: Contribution to journal › Article › peer-review
• 2007

  The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations

  Alfonso-Prieto, M., Borovik, A., Carpena, X., Murshudov, G., Melik-Adamyan, W., Fita, I., Rovira, C. & Loewen, P. C., 11 Apr 2007, In: Journal of the American Chemical Society. 129, 14, p. 4193-4205 13 p.

  Research output: Contribution to journal › Article › peer-review
• 2006

  Intensity statistics in twinned crystals with examples from the PDB

  Lebedev, A. A., Vagin, A. A. & Murshudov, G. N., Jan 2006, In: Acta crystallographica section d-Biological crystallography. 62, p. 83-95 13 p.

  Research output: Contribution to journal › Article › peer-review

• SPINE workshop on automated X-ray analysis: a progress report

  Bahar, M., Ballard, C., Cohen, S. X., Cowtan, K. D., Dodson, E. J., Emsley, P., Esnouf, R. M., Keegan, R., Lamzin, V., Langer, G., Levdikov, V., Long, F., Meier, C., Muller, A., Murshudov, G. N., Perrakis, A., Siebold, C., Stein, N., Turkenburg, M. G. W. & Vagin, A. A. & 3 others, Winn, M., Winter, G. & Wilson, K. S., Oct 2006, In: Acta Crystallographica. Section D, Biological Crystallography. 62, p. 1170-1183 14 p.

  Research output: Contribution to journal › Article › peer-review
• 2005

  Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine

  Schnick, C., Robien, M. A., Brzozowski, A. M., Dodson, E. J., Murshudov, G. N., Anderson, L., Luft, J. R., Mehlin, C., Hol, W. G. J., Brannigan, J. A. & Wilkinson, A. J., Sept 2005, In: Acta Crystallographica. Section D, Biological Crystallography. 61, p. 1245-1254 10 p.

  Research output: Contribution to journal › Article › peer-review

• Variable role of ions in two drug intercalation complexes of DNA

  Valls, N., Steiner, R. A., Wright, G., Murshudov, G. N. & Subirana, J. A., Aug 2005, In: Journal of Biological Inorganic Chemistry. 10, 5, p. 476-482 7 p.

  Research output: Contribution to journal › Article › peer-review
• 2004

  Crystallization and preliminary X-ray diffraction studies of a fungal hydrolase from Ophiostoma novo-ulmi

  Isupov, M. N., Brindley, A. A., Hollingsworth, E. J., Murshudov, G. N., Vagin, A. A. & Littlechild, J. A., Oct 2004, In: Acta crystallographica section d-Biological crystallography. 60, p. 1879-1882 4 p.

  Research output: Contribution to journal › Article › peer-review

• Developments in the CCP4 molecular-graphics project

  Potterton, L., McNicholas, S., Krissinel, E., Gruber, J., Cowtan, K., Emsley, P., Murshudov, G. N., Cohen, S., Perrakis, A. & Noble, M., Dec 2004, In: Acta Crystallographica. Section D, Biological Crystallography. 60, p. 2288-2294 7 p.

  Research output: Contribution to journal › Article › peer-review

• Direct incorporation of experimental phase information in model refinement

  Skubak, P., Murshudov, G. N. & Pannu, N. S., Dec 2004, In: Acta crystallographica section d-Biological crystallography. 60, p. 2196-2201 6 p.

  Research output: Contribution to journal › Article › peer-review

• DNA variability in five crystal structures of d(CGCAATTGCG)

  Valls, N., Wright, G., Steiner, R. A., Murshudov, G. N. & Subirana, J. A., Apr 2004, In: Acta crystallographica section d-Biological crystallography. 60, p. 680-685 6 p.

  Research output: Contribution to journal › Article › peer-review

• REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use

  Vagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F. & Murshudov, G. N., Dec 2004, In: Acta crystallographica section d-Biological crystallography. 60, p. 2184-2195 12 p.

  Research output: Contribution to journal › Article › peer-review
• 2003

  Fisher's information in maximum-likelihood macromolecular crystallographic refinement

  Steiner, R. A., Lebedev, A. A. & Murshudov, G. N., Dec 2003, In: Acta crystallographica section d-Biological crystallography. 59, p. 2114-2124 11 p.

  Research output: Contribution to journal › Article › peer-review

• The structure of NADH in the enzyme dTDP-D-glucose dehydratase (RmIB)

  Beis, K., Allard, S. T. M., Hegeman, A. D., Murshudov, G., Philp, D. & Naismith, J. H., 1 Oct 2003, In: Journal of the American Chemical Society. 125, 39, p. 11872-11878 7 p.

  Research output: Contribution to journal › Article › peer-review
• 2002

  Structural origins of the functional divergence of human insulin-like growth factor-I and insulin

  Brzozowski, A. M., Dodson, E. J., Dodson, G. G., Murshudov, G. N., Verma, C., Turkenburg, J. P., de Bree, F. M. & Dauter, Z., 30 Jul 2002, In: Biochemistry. 41, 30, p. 9389-9397 9 p.

  Research output: Contribution to journal › Article › peer-review

• Substrate distortion by a beta-mannanase: Snapshots of the Michaelis and covalent-intermediate complexes suggest a B-2,B-5 conformation for the transition state

  Ducros, V. M. A., Zechel, D. L., Murshudov, G. N., Gilbert, H. J., Szabo, L., Stoll, D., Withers, S. G. & Davies, G. J., Aug 2002, In: Angewandte Chemie International Edition. 41, 15, p. 2824-2827 4 p.

  Research output: Contribution to journal › Article › peer-review

• The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex

  Murshudov, G. N., Grebenko, A. I., Brannigan, J. A., Antson, A. A., Barynin, V. V., Dodson, G. G., Dauter, Z., Wilson, K. S. & Melik-Adamyan, W. R., Dec 2002, In: Acta Crystallographica. Section D, Biological Crystallography. 58, 12, p. 1972-1982 11 p.

  Research output: Contribution to journal › Article › peer-review

  File
• 2001

  Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis

  Ducros, V. M. A., Lewis, R. J., Verma, C. S., Dodson, E. J., Leonard, G., Turkenburg, J. P., Murshudov, G. N., Wilkinson, A. J. & Brannigan, J. A., 2 Mar 2001, In: Journal of Molecular Biology. 306, 4, p. 759-771 13 p.

  Research output: Contribution to journal › Article › peer-review

• Structure of the Bacillus cell fate determinant SpollAA in phosphorylated and unphosphorylated forms

  Seavers, P. R., Lewis, R. J., Brannigan, J. A., Verschueren, K. H. G., Murshudov, G. N. & Wilkinson, A. J., 3 Jul 2001, In: Structure. 9, 7, p. 605-614 10 p.

  Research output: Contribution to journal › Article › peer-review

• The three-dimensional structure of human S100A12

  Moroz, O. V., Antson, A. A., Murshudov, G. N., Maitland, N. J., Dodson, G. G., Wilson, K. S., Skibshoj, I., Lukanidin, E. M. & Bronstein, I. B., Jan 2001, In: Acta Crystallographica. Section D, Biological Crystallography. 57, p. 20-29 10 p.

  Research output: Contribution to journal › Article › peer-review

• Use of TLS parameters to model anisotropic displacements in macromolecular refinement

  Winn, M. D., Isupov, M. N. & Murshudov, G. N., Jan 2001, In: Acta Crystallographica. Section D, Biological Crystallography. 57, 1, p. 122-133 12 p.

  Research output: Contribution to journal › Article › peer-review

• X-ray structure of bovine pancreatic phospholipase A(2) at atomic resolution

  Steiner, R. A., Rozeboom, H. J., de Vries, A., Kalk, K. H., Murshudov, G. N., Wilson, K. S. & Dijkstra, B. W., Apr 2001, In: Acta Crystallographica. Section D, Biological Crystallography. 57, p. 516-526 11 p.

  Research output: Contribution to journal › Article › peer-review

• 2000

  Crystal structure of dodecameric vanadium-dependent bromoperoxidase from the red algae Corallina officinalis

  Isupov, M. N., Dalby, A. R., Brindley, A. A., Izumi, Y., Tanabe, T., Murshudov, G. N. & Littlechild, J. A., 16 Jun 2000, In: Journal of Molecular Biology. 299, 4, p. 1035-1049 15 p.

  Research output: Contribution to journal › Article › peer-review

• Structure of a slow processing precursor penicillin acylase from Escherichia coli reveals the linker peptide blocking the active-site cleft

  Hewitt, L., Kasche, V., Lummer, K., Lewis, R. J., Murshudov, G. N., Verma, C. S., Dodson, G. G. & Wilson, K. S., 29 Sept 2000, In: Journal of Molecular Biology. 302, 4, p. 887-898 12 p.

  Research output: Contribution to journal › Article › peer-review

• The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5

  Sabini, E., Schubert, H., Murshudov, G., Wilson, K. S., Siika-Aho, M. & Penttila, M., Jan 2000, In: Acta Crystallographica. Section D, Biological Crystallography. 56, p. 313 11 p.

  Research output: Contribution to journal › Article › peer-review

• 1999

  Binding of non-catalytic ATP to human hexokinase I highlights the structural components for enzyme-membrane association control

  Rosano, C., Sabini, E., Rizzi, M., Deriu, D., Murshudov, G., Bianchi, M., Serafini, G., Magnani, M. & Bolognesi, M., 15 Nov 1999, In: Structure. 7, 11, p. 1427-1437 11 p.

  Research output: Contribution to journal › Article › peer-review

• Efficient anisotropic refinement of macromolecular structures using FFT

  Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S. & Dodson, E. J., Jan 1999, In: Acta crystallographica section d-Biological crystallography. 55, p. 247-255 9 p.

  Research output: Contribution to journal › Article › peer-review

• Solution of the structure of the cofactor-binding fragment of CysB: A struggle against non-isomorphism

  Verschueren, K. H. G., Tyrrell, R., Murshudov, G. N., Dodson, E. J. & Wilkinson, A. J., Feb 1999, In: Acta Crystallographica. Section D, Biological Crystallography. 55, p. 369-378 10 p.

  Research output: Contribution to journal › Article › peer-review

• The structure of the exo-beta-(1,3)-glucanase from Candida albicans in native and bound forms: Relationship between a pocket and groove in family 5 glycosyl hydrolases

  Cutfield, S. M., Davies, G. J., Murshudov, G., Anderson, B. F., Moody, P. C. E., Sullivan, P. A. & Cutfield, J. F., 3 Dec 1999, In: Journal of Molecular Biology. 294, 3, p. 771-783 13 p.

  Research output: Contribution to journal › Article › peer-review

• 1998

  BLANC: the program suite for protein crystallography

  Vagin, A. A., Murshudov, G. N. & Strokopytov, B. V., 1 Feb 1998, In: Journal of Applied Crystallography. 31, p. 98-102 5 p.

  Research output: Contribution to journal › Article › peer-review

• Incorporation of prior phase information strengthens maximum-likelihood structure refinement

  Pannu, N. S., Murshudov, G. N., Dodson, E. J. & Read, R. J., 1 Nov 1998, In: Acta crystallographica section d-Biological crystallography. 54, p. 1285-1294 10 p.

  Research output: Contribution to journal › Article › peer-review

• Stabilizing bound O-2 in myoglobin by valine(68) (E11) to asparagine substitution

  Krzywda, S., Murshudov, G. N., Brzozowski, A. M., Jaskolski, M., Scott, E. E., Klizas, S. A., Gibson, Q. H., Olson, J. S. & Wilkinson, A. J., 10 Nov 1998, In: Biochemistry. 37, 45, p. 15896-15907 12 p.

  Research output: Contribution to journal › Article › peer-review

• Validation tools: can they indicate the information content of macromolecular crystal structures?

  Dodson, E. J., Davies, G. J., Lamzin, V. S., Murshudov, G. N. & Wilson, K. S., 15 Jun 1998, In: Structure. 6, 6, p. 685-690 6 p.

  Research output: Contribution to journal › Article › peer-review

• Who checks the checkers? Four validation tools applied to eight atomic resolution structures

  Wilson, K. S., Butterworth, S., Dauter, Z., Lamzin, V. S., Walsh, M., Wodak, S., Pontius, J., Richelle, J., Vaguine, A., Sander, C., Hooft, R. W. W., Vriend, G., Thornton, J. M., Laskowski, R. A., MacArthur, M. W., Dodson, E. J., Murshudov, G., Oldfield, T. J., Kaptein, R. & Rullmann, J. A. C. & 1 others, EU 3-D Validation Network, 20 Feb 1998, In: Journal of Molecular Biology. 276, 2, p. 417-436 20 p.

  Research output: Contribution to journal › Article › peer-review

• 1997

  Refinement of macromolecular structures by the maximum-likelihood method

  Murshudov, G. N., Vagin, A. A. & Dodson, E. J., 1 May 1997, In: Acta crystallographica section d-Biological crystallography. 53, p. 240-255 16 p.

  Research output: Contribution to journal › Article › peer-review

• The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement

  Tyrrell, R., Verschueren, K. H. G., Dodson, E. J., Murshudov, G. N., Addy, C. & Wilkinson, A. J., 15 Aug 1997, In: Structure. 5, 8, p. 1017-1032 16 p.

  Research output: Contribution to journal › Article › peer-review

• 1996

  Structure of the heme d of Penicillium vitale and Escherichia coli catalases

  Murshudov, G. N., Grebenko, A. I., Barynin, V., Dauter, Z., Wilson, K. S., Vainshtein, B. K., MelikAdamyan, W., Bravo, J., Ferran, J. M., Ferrer, J. C., Switala, J., Loewen, P. C. & Fita, I., 12 Apr 1996, In: Journal of Biological Chemistry. 271, 15, p. 8863-8868 6 p.

  Research output: Contribution to journal › Article › peer-review

• 1995

  The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands

  Tame, J. R. H., Dodson, E. J., Murshudov, G., Higgins, C. F. & Wilkinson, A. J., 15 Dec 1995, In: Structure. 3, 12, p. 1395-1406 12 p.

  Research output: Contribution to journal › Article › peer-review

• 1994

  CRYSTAL-STRUCTURE OF AN EXTRACELLULAR FRAGMENT OF THE RAT CD4 RECEPTOR-CONTAINING DOMAIN-3 AND DOMAIN-4

  Lange, G., Lewis, S. J., Murshudov, G. N., Dodson, G. G., Moody, P. C. E., Turkenburg, J. P., Barclay, A. N. & Brady, R. L., 15 Jun 1994, In: Structure. 2, 6, p. 469-481 13 p.

  Research output: Contribution to journal › Article › peer-review

• THE STRUCTURAL BASIS OF SEQUENCE-INDEPENDENT PEPTIDE BINDING BY OPPA PROTEIN

  TAME, J. R. H., MURSHUDOV, G. N., DODSON, E. J., NEIL, T. K., DODSON, G. G., HIGGINS, C. F. & WILKINSON, A. J., 10 Jun 1994, In: Science. 264, 5165, p. 1578-1581 4 p.

  Research output: Contribution to journal › Article › peer-review

• 1992

  3-DIMENSIONAL STRUCTURE OF CATALASE FROM MICROCOCCUS LYSODEIKTICUS AT 1.5 Å RESOLUTION

  MURSHUDOV, G. N., MELIKADAMYAN, W. R., GREBENKO, A. I., BARYNIN, V. V., VAGIN, A. A., VAINSHTEIN, B. K., DAUTER, Z. & WILSON, K. S., 9 Nov 1992, In: FEBS Letters. 312, 2-3, p. 127-131 5 p.

  Research output: Contribution to journal › Article › peer-review

• THE POLYPEPTIDE CHAIN FOLD IN TYROSINE PHENOL-LYASE, A PYRIDOXAL-5'-PHOSPHATE DEPENDENT ENZYME

  ANTSON, A. A., STROKOPYTOV, B. V., MURSHUDOV, G. N., ISUPOV, M. N., HARUTYUNYAN, E. H., DEMIDKINA, T. V., VASSYLYEV, D. G., DAUTER, Z., TERRY, H. & WILSON, K. S., 18 May 1992, In: FEBS Letters. 302, 3, p. 256-260 5 p.

  Research output: Contribution to journal › Article › peer-review