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Laboratory of Macromolecular Crystallography


Publications by A.G.Urzhumtsev

At 2003, January 01

The full texts of papers, preprints and theses may be found here.

Papers in journals

  • Urzhumtsev, A. & Urzhumtseva, L. (2002) " SF2CNS: general purpose program to calculate CNS-formatted maps easily", J. Appl. Cryst., 35, 750.

  • Lunin, V.Y., Afonine P.V. & Urzhumtsev, A.G. (2002). "Likelihood-based refinement. I. Irremovable model errors". Acta Cryst. A58, 270-282.

  • Lunin, V.Y., Urzhumtsev, A. & Bockmayr, A. (2002). "Direct phasing by binary integer programming". Acta Cryst. A58, 283-291.

  • Urzhumtsev, A. & Urzhumtseva, L. (2002).. "Multiple rotation function". Acta Cryst, D58, 2066-2075.

  • Fokine, A. & Urzhumtsev, A.G. (2002). "On the use of low resolution data for translation search in molecular replacement". Acta Cryst., A58, 72-74.

  • Fokine, A. & Urzhumtsev, A. (2002). "Flat bulk solvent model: getting optimal parameters". Acta Cryst., D58 , 1387-1392.

  • Urzhumtseva, L. & Urzhumtsev, A. (2002). "COMPANG : program for comparative analysis of rotation angles". J. Appl.Cryst., 35, 644-647.

  • Lunin, V.Y., Lunina, N.L., Ritter, S., Frey, I., Berg, A., Diderichs, K., Podjarny, A.D., Urzhumtsev, A. & Baumstark M.W. "Low-resolution data analysis for low-density lipoprotein particle". (2001). Acta Cryst., D57, 108-121.

  • Urzhumtsev, A.G. & Lunin, V.Y. "Fast differentiation algorithm and efficient calculation of the exact matrix of second derivatives". (2001). Acta Cryst.. A57, 451-460.

  • Lunin, V.Y., Lunina, N.L. & Urzhumtsev, A.G. (2000). "Connectivity properties of high-density regions and ab initio phasing at low resolution". Acta Cryst. A56, 375-382.

  • Lunin, V.Y., Lunina, N.L., Petrova, T.E., Skovoroda, T.P., Urzhumtsev, A.G. & Podjarny, A.D. (2000). "Low-resolution ab initio phasing: problems and advances". Acta Cryst. D56, 1223-1232.

  • Urzhumtsev, A.G., Lunina, N.L., Skovoroda, T.P., Podjarny, A.D. & Lunin, V.Y. (2000). "Density constraints and low-resolution phasing". Acta Cryst. D56, 1233-1244.

  • Brino, L., Urzhumtsev, A.G., Mousli, M., Mitschler, A., Bergdoll, M., Oudet, P. & Moras, D. (2000). "Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center". J.Biol.Chem., 275, 9468-9475.

  • Urzhumtseva, L.M. & Urzhumtsev, A.G. (2000). "Tcl/Tk based programs. IV. CALCRYS: crystallographic calculator". J.Appl. Cryst., 33, 992-992.

  • Lunin, V.Y., Lunina, N.L. & Urzhumtsev, A.G. (1999). "Seminvariant density decomposition and connectivity analysis and their application to very low resolution macromolecular phasing". Acta Cryst. A55, 916-925.

  • Urzhumtseva, L.M. & Urzhumtsev, A.G. (1999). "Tcl/Tk based programs. III. CRITXPL: graphical analysis of the X-PLOR refinement log-files". J.Appl. Cryst., 32, 376-377.

  • Lunin, V.Yu., Lunina, N.L., Petrova, T.E., Urzhumtsev A.G. & Podjarny A.D. (1998). "On the Ab initio solution of the Phase Problem for Macromolecules at Very Low Resolution. II. Generalized Likelihood Based Approach to Cluster Discrimination". Acta Cryst. D54, 726-734.

  • Urzhumtsev, A., Tete-Favier, F., Mitschler, A., Barbanton, J., Barth, P., Urzhumtseva, L., Biellmann, J-F., Podjarny, A.D. & Moras, D. (1997). "A 'specificity' pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil ". Structure, 5, 5, 601-612.

  • Urzhumtseva, L.M. & Urzhumtsev, A.G. (1997). "Tcl/Tk-based programs. II. CONVROT: a program to recalculate different rotation descriptions". J.Appl.Cryst., 30, 402-410.

  • Urzhumtsev, A.G. (1997). "Local improvement of electron density maps". Acta Cryst., D53, 540-543.

  • Podjarny, A.D., Howard, E.I., Urzhumtsev, A.G. & Grigera, J.R. (1997). "A Multicopy Modelling of the Water Distribution in Macromolecular Crystals". Proteins, 28, 303-312.

  • Urzhumtsev, A.G., Skovoroda, T.P. & Lunin, V.Yu. (1996). "A procedure compatible with X-PLOR for the calculation of electron-density maps weighted using an R-free-likelihood-based approach". J.Appl.Cryst., 29, 741-744.

  • Urzhumtsev, A.G., Vernoslova, E.A. & Podjarny, A.D. (1996). "Approaches to Very Low Resolution Phasing of the Ribosome 50S particle from Thermus thermophilus by the Few-Atoms-Models and Molecular-Replacement Methods". Acta Cryst., D52,1092-1097.

  • Lunin, V.Yu., Lunina, N.L., Petrova, T.E., Vernoslova, E.A., Urzhumtsev, A.G. & Podjarny, A.D. (1995) "On the ab-initio Solution of the Phase Problem for Macromolecules at Very Low Resolution: the Few Atoms Model Method". Acta Cryst., D51, 896-903.

  • Urzhumtsev, A.G. & Podjarny, A.D. (1995). "On the Solution of the Molecular Replacement Problem at Very Low Resolution: Application to Large Complexes". Acta Cryst., D51, 888-895.

  • Tete-Favier, F., Barth, P., Mitchler, A., Podjarny, A.D., Rondeau, J.-M., Urzhumtsev, A., Biellmann, J.-F. & Moras, D. (1995). "Aldose Reductase from Pig Lens". European Journal of Medicinal Chemistry, 30, S, 589-603.

  • Urzhumtsev, A.G. & Podjarny, A.D. (1994). "Programs for translation searches with two independent models simultaneously". J.Appl.Cryst., 27, 122-124.

  • Morgunova, E.Yu., Mikhailov, A.M., Urzhumtsev, A.G. & Vainstein, B.K. (1992). "Crystal structure of the CMtV capsid at 6A resolution". Kristallografiya, 37, 2, 396-404. (In Russian)

  • Chirgadze, Yu.N., Nevskaya, N.A., Vernoslova, E.A., Nikonov, S.V., Sergeev, Yu.V., Brazhnikov, E.V., Fomenkova, N.P., Lunin, V.Yu. & Urzhumtsev, A.G. (1991). "Crystal structure of calf eye lens gamma-crystalline IIIb at 2.5A resolution: its relation to function". Experimental Eye Research, 53, 295-304.

  • Chirgadze, Yu.N., Brazhnikov, E.V., Nikonov, S.V., Fomenkova, N.P., Garber, M.B., Urzhumtsev, A.G. Lunin, V.Yu., , Chirgadze, N.Yu. & Nekrasov, Yu.V. (1991). "Crystal structure of ribosomal factor G from bacteria Thermus thermophilus at low resolution". Dokl.Acad.Nauk SSSR, 320, 488-491. (In Russian)

  • Urzhumtsev, A.G. (1991). "How to calculate planarity restraints". Acta Cryst., A47, 723-727.

  • Urzhumtsev, A.G. (1991). "Low-resolution phases: influence on SIR-syntheses and retrieval with double-step filtration". Acta Cryst., A47, 794-801.

  • Lunin, V.Yu., Urzhumtsev, A.G. & Skovoroda, T.A. (1990). "Direct low-resolution phasing from electron-density histograms in protein crystallography". Acta Cryst., A46, 540-544.

  • Lobsanov, Yu.D., Pletnev, V.Z., Vtyurin, N.N., Lubnin, M.Yu., Mokulskii, M.A., Urzhumtsev, A.G., Lunin, V.Yu. & Luzyanina, T.B. (1990). "X-ray study of the pea lectin-carbohydrate complex at 2.4A resolution. I. Atomic model". Bioorganic Chemistry (USSR), 16, 12, 1589-1598. (In Russian)

  • Urzhumtsev, A.G., Lunin, V.Yu. & Luzyanina, T.B. (1989). "Bounding a Molecule in a Noisy Synthesis". Acta Cryst., A45, 34-39.

  • Urzhumtsev, A.G., Lunin, V.Yu. & Vernoslova, E.A. (1989). "FROG - high-speed restraint-constraint refinement program for macromolecular structure". J.Appl.Cryst., 22, 500-506.

  • Chirgadze, Yu.N., Nevskaya, N.A., Fomenkova, N.P., Nikonov, S.V., Sergeev, Yu.V., Brazhnikov, E.V., Garber, M.B., Lunin, V.Yu., Urzhumtsev, A.G. & Vernoslova, E.A. (1986). "Spatial structure of gamma-crystalline IIIb from calf lens at 2.5A resolution". Dokl.Akad.Nauk SSSR, 290, 2, 492-495. (In Russian)

  • Lunin, V.Yu., Urzhumtsev, A.G., Vernoslova, E.A., Chirgadze, Yu.N., Nevskaya, N.A.& Fomenkova, N.P. (1985). "Phase Improvement in Protein Crystallography Using a Mixed Electron Density Model". Acta Cryst., A41, 166-171.

  • Lunin, V.Yu. & Urzhumtsev, A.G. (1985). "Program construction for macromolecule atomic model refinement based on the fast Fourier transform and fast differentiation algorithms". Acta Cryst., A41, 327-333.

  • Lunin, V.Yu. & Urzhumtsev, A.G. (1984). "Improvement of Protein Phases by Coarse Model Modification". Acta Cryst., A40, 269-277.

  • Lunin, V.Yu. & Urzhumtsev, A.G. (1983). "Improvement of electron density maps for proteins using atomic model structure". Kristallografiya (SSSR), 28, 310-315. (In Russian)

The full texts of papers

Papers in digest

  • Lunin, V.Y., Urzhumtsev, A. & Bockmayr, A. (2002). "Direct phasing by Binary integer programming and its use for envelope determination". CCP4 Newsletter on Protein Crystallography, 40_12.

  • Afonine, P., Lunin, V.Y. & Urzhumtsev, A.G. (2002). "Search of the optimal strategy for refinement of atomic models". CCP4 Newsletter on Protein Crystallography, 40_14.

  • Fokine, A. & Urzhumtsev, A.G. (2002). "Bulk solvent correction for yet unsolved structures". CCP4 Newsletter on Protein Crystallography, 40.

  • Afonine, P., Pichon-Pesme, V., Muzet, N., Lecomte, C. & Urzhumtsev, A. (2002). "Modelling of bond electrons by Gaussian scatters at subatomic resolution". CCP4 Newsletter on Protein Crystallography, 41.

  • Afonine, P., Lunin, V.Y. & Urzhumtsev, A.G. (2001). "Maximum-likelihood refinement of atomic models using least-squares criterion". CCP4 Newsletter on protein crystallography, 39, 52-56.

  • Urzhumtsev, A.G. & Lunin, V.Y. (2001). "Efficient calculation of the exact matrix of the second derivatives". CCP4 Newsletter on protein crystallography, 39, 60-67.

  • Lunin, V.Y., Podjarny, A.D. & Urzhumtsev, A. (2001). "Low-resolution phasing in macromolecular crystallography". In : Advances in Structure Analysis, CSCA, Prague, Czech Republic, R.Kuzel & J.Hasek, eds., 4-36.

  • Urzhumtsev, A., Podjarny, A., Lunin, V.Y. (2001). "Ab initio phasing starting from low resolution". Invited article. Euroconference on Phasing, 23-27 June 2001, Martina Franca, Italy, 4.35-4.40.

  • Podjarny, A.D., Urzhumtsev, A. & Uson, I. (2001). "Ab-initio methods for structure determination". In : Advances in Structure Analysis, CSCA, Prague, Czech Republic, R.Kuzel & J.Hasek, eds., 1-3.

  • Fokine, A. & Urzhumtsev, A.G. (2001). "Improvement of noisy maps by bulk solvent correction". CCP4 Newsletter on Protein Crystallography, 39, 71-78.

  • Urzhumtseva, L. & Urzhumtsev, A.G. (2001). "Multiple rotation function". CCP4 Newsletter on Protein Crystallography, 39, 79-85.

  • Urzhumtsev, A.G. (2000). "Modelling of disordered solvent in macromolecular crystals". CCP4 Newsletter on Protein Crystallography, 38, 38-49.

  • Lunin, V.Y. & Urzhumtsev, A.G. (1999). "Maximal Likelihood Refinement. It works, but why?". CCP4 Newsletter on Protein Crystallography, 37, 14-28.

  • Urzhumtseva, L.M. & Urzhumtsev, A.G. (1999). "Tcl/tk based programs : crystallographic calculator". CCP4 Newsletter on Protein Crystallography, 37, 5-6.

  • Urzhumtseva, L.M. & Urzhumtsev, A.G. (1998). "Programs Tcl/Tk based crystallographic software : current state and new programs". CCP4 Newsletter on Protein Crystallography, 35, 22-24.

  • Urzhumtsev, A.G., Podjarny, A.D. & Lunin, V.Y. (1998). "On density modification at very low resolution". CCP4 Newsletter on Protein Crystallography, 35, 25-33.

  • Podjarny, A.D., Urzhumtsev, A.G. & Lunin, V.Y. (1997). "Model based low resolution phasing". Iin Direct Methods for Solving Macromolecular Structures, ed. S.Fortier, NATO ASI Series C, Vol.507, 421-431.

  • Urzhumtsev, A.G., Lunin, V.Yu. & Podjarny, A.D. (1997). "Low resolution crystallographic images". In Recent Advances in Phasing, Ed. By K.S.W.Wilson, G.Davies, A.W.Ashton & S.Bailey, Proceedings of the CCP4 Study Weekend, University of York, 3-4 January, 1997, 207-214.

  • Podjarny, A.D. & Urzhumtsev, A.G. (1997). "Low resolution phasing". In Methods in Enzymology, Academic Press, San Diego., C.W.Carter, Jr., R.M.Sweet, eds. 276A, 641-658.

  • Urzhumtsev, A.G. (1996). "Density growing : a method for local improvement of electron density maps". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 32b, 36-39.

  • Urzhumtsev, A.G. (1996). "Relations between some rotation descriptions for molecular replacement procedure". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 32b, 43-46.

  • Urzhumtseva, L.M. & Urzhumtsev, A.G. (1996). "Tcl/Tk-based programs. I. CONFOR - user-friendly converter for crystallographic data files". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 32b, 40-42.

  • Podjarny, A.D., Rees, B. & Urzhumtsev, A.G. (1996). "Density modification in X-ray crystallography". In Methods in Molecular Biology, v.56 : "Crystallographic Methods and Protocols", ed. C.Jones, B.Milloy, M.R.Sanderson, Totowa, New Jersey : Humana Press, 205-226.

  • Urzhumtsev, A.G. & Podjarny, A.D. (1995). "On the problem of solvent modeling in macromolecular crystals using diffraction data: 1.The low-resolution range". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, 12-16.

  • Volkmann, N., Schlunzen, F., Urzhumtsev, A.G., Vernoslova, E.A., Podjarny, A.D., Roth, M., Pebay-Peyroula , E., Berkovitch-Yellin, Z., Zaytzev-Bashan, A. & Yonath, A. (1995). "On ab-initio phasing of ribosomal particles at very low resolution". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, 23-32.

  • Ivanov, M.E., Urzhumtsev, A.G. (1995). "FROG PC - a menu-based environment for atomic model refinement program on a personal computer". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, 20-22.

  • Lunin, V.Yu., Lunina, N.L., Petrova, T.E., Vernoslova, E.A., Urzhumtsev, A.G. & Podjarny, A.D. (1994). "On the ab-initio solution of the phase problem for macromolecules at very low resolution. The Few Atoms Model method". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 30, 37-44.

  • Vernoslova, E.A. & Urzhumtsev, A.G. (1994). "Current development in the program package FROG for atomic model refinement". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 30, 27-28.

  • Urzhumtsev, A.G., Podjarny, A.D. & Navaza, J. (1994). "On the solution of the molecular replacement problem at very low resolution". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 30, 29-36.

  • Urzhumtseva, L.M. & Urzhumtsev, A.G. (1994). "Published methods in crystallography. Reference database on personal computers". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 30, 45-47.

  • Podjarny, A.D., Urzhumtsev, A.G. & Navaza, J. (1994). "On the solution of the molecular replacement problem at very low resolution: application to a ribosome model crystal". ACA Transactions, 30, 109-120.

  • Urzhumtsev, A.G. (1992). "On the reliability of atomic models in the PDB: stereochemical point of view". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 27, 31-32.

  • Urzhumtsev, A.G., Lunin, V.Yu. & Vernoslova, E.A. (1990). "New refinement program FROG gives new possibilities to study macromolecular models". Proc.of the First Intern. Meeting on Structure and Chemistry of Ribonucleases, Moscow, USSR, December 1989, 410-415.

  • Urzhumtsev, A.G., Lunin, V.Yu. & Vernoslova, E.A. (1989). "The program complex FROG for local refinement of atomic structures of macromolecules". In Computing methods of protein engineering, Software, Institute of Mathematics AS BSSR & Institute of biochemistry, 86, 86-97, Minsk. (In Russian)

The full texts of papers

Preprints & Software

  • Urzhumtsev, A.G., Lunin, V.Yu. & Vernoslova, E.A. (1988). "Program package FROG". Software, FORTRAN, 10, NCBI AN SSSR, Pushchino, Russia. (In Russian)

  • Urzhumtsev, A.G. (1985). "Using of local averaging for protein image analysis in electron density maps". Preprint, NCBI AN SSSR, Pushchino, Russia (In Russian)

  • Lunin, V.Yu., Urzhumtsev, A.G., Vernoslova, E.A., Chirgarze, Yu.N., Fomenkova, N.P. & Nevskaya, N.A. (1984). "Using of atomic mixed model for phase improvement in protein crystallography". Preprint, NCBI AN SSSR, Pushchino, Russia. (In Russian)

  • Lunin, V.Yu. & Urzhumtsev, A.G. (1983). "Program construction for macromolecular atomic model refinement based on Fast Fourier and Fast Differentiation algorithms". Preprint, NCBI AN SSSR, Pushchino. (In Russian)

  • Urzhumtsev, A.G. & Lunin, V.Yu. (1982). "Electron-density-maps improvement by use of refinement of atomic model structure. II. Phase improvement for ?-crystalline". Preprint, NCBI AN SSSR, Pushchino. (In Russian)

  • Lunin, V.Yu. & Urzhumtsev, A.G. (1981). "Electron-density-maps improvement by use of refinement of atomic model structure. I. The method's description". Preprint, NCBI AN SSSR, Pushchino. (In Russian)

The full texts of papers

Theses

  • Urzhumtsev, A. (1996). "Developpement de methodes et logiciels pour la determination de structures macromoleculaires par radiocristallographie. Applications e differents projets". Synthese d'activite scientifique, IGBMC, Strasbourg, 1996.

  • Urzhumtsev, A.G. (1985). "Using a mixed atomic model for structure-factor phases improvement in protein crystallography". Resume of Ph.D.Theses, Moscow, Russia. (In Russian)

  • Urzhumtsev, A.G. (1985). "Using a mixed atomic model for structure-factor phases improvement in protein crystallography". Ph.D.Theses, Institute of Crystallography, Moscow, Russia (In Russian)

The full texts of papers

Abstracts

  • Afonine, P., Lunin, V.Y. & Urzhumtsev, A. (2002). "Quadratic approximation of the maximum-likelihood criterion ". Acta Cryst., A58, S, C263 [Collected Abstracts, XIXth IUCr Congress & General Assembly, 6-15 August 2002, Geneve, Switzerland, 263].

  • Afonine, P. & Urzhumtsev, A. (2002). "Affinement par moindres carres et par vraisemblance maximale" Journee de l'Ecole Doctorale EMMA, 23 Avril 2002, Nancy, 48-51.

  • Fokine, A., Lunina, N., Lunin, V.Y. & Urzhumtsev, A. (2002). "Bulk solvent and its role in macromolecular phasing". Acta Cryst., A58, S, C267 [Collected Abstracts, XIXth IUCr Congress & General Assembly, 6-15 August 2002, Geneve, Switzerland, 267].

  • Fokine, A. & Urzhumtsev, A. (2002). "Modelisation du solvant desordonne dans de cristaux macromoleculaires". Journee de l'Ecole Doctorale EMMA, 23 Avril 2002, Nancy, 71-73.

  • Urzhumtsev, A., Lunin, V.Yu., Lunina, N.L., Ritter, S., Frey, I., Keul, J., Diederichs, K., Podjarny, A. & Baumstark, M. (2002). "LDL particle : Direct structure determination". Collected Abstracts, ACA Meeting, 25-30 May 2002, San Antonio, USA, 33.

  • Urzhumtsev, A., Lunina, N., Chabriere, E. & Lunin, V.Y. (2002). "Direct phasing in crystallography : connectivity of electron density maps". Z. Krist., Suppl., 19, 16. [Collected Abstracts, DGK Meeting, 4-7 March 2002, Kiel, Germany].

  • Urzhumtsev, A., Lunina, N.L. & Lunin, V.Y. (2002). "The connectivity-based choice in macromolecular low resolution ab-initio phasing". Acta Cryst., A58, S, C43 [Collected Abstracts, XIXth IUCr Congress & General Assembly, 6-15 August 2002, Geneve, Switzerland, 43].

  • Urzhumtsev, A. & Urzhumtseva, L. (2002). "Fonction de rotation multiple et logiciel COMPANG". GTBio-02, 16-19 Oct. 2002, Marseille, France, CO31.

  • Urzhumtseva, L. & Urzhumtsev, A. (2002). "Multiple rotation function for Molecular Replacement". Acta Cryst., A58, S, C78 [Collected Abstracts, XIXth IUCr Congress & General Assembly, 6-15 August 2002, Geneve, Switzerland, 78].

  • Afonine, P., Lunin, V.Y. & Urzhumtsev, A.G. (2001). Maximum-likelihood refinement of atomic models using least-squares criterion. Euroconference on Phasing Biological Macromolecules (Phabio). Martina Franca - Italy, June 23-27, 2001, 4.47-4.51.

  • Afonine, P., Lunin, V.Y. & Urzhumtsev, A.G. (2001). "Simulation du critere de vraisemblance maximale par le critere de moindre carre". AFC2001 Colloque de l'Association Francaise de Cristallographie, Orsay,3-6 juillet 2001, 97.

  • Afonine, P., Lunin, V.Y. & Urzhumtsev, A. (2001). "Maximum-likelihood refinement of atomic models using least squares criterion". ECM-20 Abstracts, XXth European Cryst.Meeting, 25-31 August 2001, Krakow, Poland, 148.

  • Chabriere, E., Lunina, N., Lunin, V.Y. & Urzhumtsev, A. (2001). "From low resolution to secondary structure elements". ECM-20 Abstracts, XXth European Cryst.Meeting, 25-31 August 2001, Krakow, Poland, 70.

  • Chabriere, E., Lunina, N., Urzhumtsev, A.G. & Lunin, V.Y. (2001). "Phasage ab initio par criteres de connectivite: de la basse resolution aux structures secondaires". AFC2001 Colloque de l'Association Francaise de Cristallographie, Orsay,3-6 juillet 2001, 99.

  • Fokine, A. & Urzhumtsev, A. (2001). "Improvement of electron density maps using a model for the bulk solvent". Euroconference on Phasing Biological Macromolecules (Phabio). Martina Franca - Italy, June 23-27, 2001, 4.43-4.43.

  • Fokine, A. & Urzhumtsev, A. (2001). "Amelioration des cartes de densite electronique par utilization d'un modele du solvant mal ordonne". AFC2001 Colloque de l'Association Francaise de Cristallographie, Orsay,3-6 juillet 2001, 96.

  • Lunin, V.Y., Urzhumtsev, A.G. & Podjarny, A.D. (2001). "Phasage ab initio a basse resolution". AFC2001 Colloque de l'Association Francaise de Cristallographie, Orsay,3-6 juillet 2001, 95.

  • Morales, R., Viguie, N., Ferrer, J.L., Urzhumtsev, A. Fontecilla-Camps, J.C., Masson, P. & Chabriere, E. (2001). "Etude cristallographique de la paraoxonase humaine". AFC2001 Colloque de l'Association Francaise de Cristallographie, Orsay,3-6 juillet 2001, 128.

  • Urzhumtsev, A., Podjarny, A. & Lunin, V.Y. (2001). Ab initio phasing starting from low resolution. Euroconference on Phasing Biological Macromolecules (Phabio). Martina Franca - Italy, June 23-27, 2001, 4.35-4.40.

  • Urzhumtseva, L. & Urzhumtsev, A.G. (2001). "Multiple rotation function". Euroconference on Phasing Biological Macromolecules (Phabio). Martina Franca - Italy, June 23-27, 2001, 4.53-4.59.

  • Urzhumtseva, L. & Urzhumtsev, A.G. (2001). "Fonction de Rotation Multiple ". AFC2001 Colloque de l'Association Francaise de Cristallographie, Orsay,3-6 juillet 2001, 98.

  • Lunin, V.Y., Lunina, N.L., Podjarny, A.D., Ritter, S., Frey, I., Keul, J., Diederichs, K., Baumstark, M.W. & Urzhumtsev, A.G. (2000). "Structure of human low density lipoprotein (LDL) at low resolution: ab initio phasing methods for structure determination". ECM19 Satellite Meeting "Frontiers in macromolecular crystallography", Bishenberg, August, 31-September, 3, France, 31.

  • Lunin, V.Y. & Urzhumtsev, A. (2000). "Maximal Likelihood refinement. It works, but why?". 19th European Crystallographic Meeting, Abstract book, 25th-31st August 2000 Nancy, France, 201.

  • Lunin, V. Y. & Urzhumtsev, A. G. (2000). "Maximal Likelihood refinement. It works, but why?". Acta Cryst. A56, S, S201.

  • Lunina, N., Lunin, V.Y., Podjarny, A., Ritter, S., Frey, I., Keul, J., Diederichs, K., Baumstark, M. & Urzhumtsev, A. (2000). "Structure of human low density lipoprotein (LDL) at low resolution: structure determination and analysis". ECM19 Satellite Meeting "Frontiers in macromolecular crystallography", Bishenberg, August, 31-September, 3, France, 32.

  • Lunina, N.L., Lunin V.Y. & Urzhumtsev A.G. (2000). "Use of map connectivity properties in macromolecular ab-initio phasing". 19th European Crystallographic Meeting, Abstract book, 25th-31st August 2000 Nancy, France, 62.

  • Lunina, N.L., Lunin, V.Y. & Urzhumtsev, A.G. (2000). "Use of map connectivity properties in macromolecular ab-initio phasing". Acta Cryst. A56, S, S62.

  • Ritter, S., Lunina, N.L., Lunin, V.Y., Urzhumtsev, A.G., Podjarny, A.D., Frey, I., Diederichs, K. & Baumstark, M.W. (2000). "Crystallization and structure determination of human low density lipoprotein (LDL) at low resolution, using ab initio phases". 19th European Crystallographic Meeting, Abstract book, 25th-31st August 2000 Nancy, France, 299.

  • Ritter, S., Lunina, N.L., Lunin, V.Y., Urzhumtsev, A.G., Podjarny, A.D., Frey, I., Diederichs, K. & Baumstark, M.W. (2000). "Crystallization and structure determination of human low density lipoprotein (LDL) at low resolution, using ab initio phases". Acta Cryst. A56, S, S299.

  • Urzhumtsev, A., Lunin, V.Y. & Lunina, N. (2000). "Density constraints and direct phasing". 19th European Crystallographic Meeting, Abstract book, 25th-31st August 2000 Nancy, France, 108.

  • Urzhumtsev, A., Lunin, V.Y. & Lunina, N. (2000). "Density constraints and direct phasing". Acta Cryst. A56, S, S108.

  • Urzhumtsev, A.G., Podjarny, A. & Lunin, V.Y. (2000). "Direct phasing at low resolution: current state and expectations". Millennium Symposium on Structural Biology, 26-29 March 2000, Heidelberg, Germany, Collected Abstracts, 103.

  • Urzhumtseva, L. & Urzhumtsev, A.G. (2000). "CALCRYS, a new programs in the Tcl/Tk based crystallographic package". 19th European Crystallographic Meeting, Abstract book, 25th-31st August 2000 Nancy, France, 198.

  • Urzhumtseva, L. & Urzhumtsev, A.G. (2000). "CALCRYS, a new programs in the Tcl/Tk based crystallographic package". Acta Cryst. A56, S, S198.

  • Lunin, V.Y., Urzhumtsev, A.G. & Podjarny, A.D. (1999). "Low resolution phasing. Achievements and perspectives". XVIII Congress and General Assembly of IUCr, Glasgow, Scotland, UK, August 4-13, 1999. Collected Abstracts, 121.

  • Lunina, N.L., Lunin, V.Y. & Urzhumtsev, A.G. (1999). "The connectivity-based choice in macromolecular low resolution ab-initio phasing". XVIII Congress and General Assembly of ICU, Glasgow, Scotland, UK, August 4-13, 1999. Collected Abstracts, 123.

  • Urzhumtsev, A.G. (1999) "Solvent modelling at low resolution". XVIII Congress and General Assembly of IUCr, Glasgow, Scotland, UK, August 4-13, 1999. Collected Abstracts, 122.

  • Urzhumtsev, A.G., Lunina, N. & Lunin, V. (1999). "Proprietes Topologiques et Phasage Direct". GTBio-99, 12-15 Oct. 1999,Hourtin (Bordeaux, France), CO31.

  • Lunin, V.Yu., Lunina, N.L., Petrova, T.E., Urzhumtsev, A.G. & Podjarny A.D. (1998). "Very low resolution ab-initio phasing. Problems and advances". Eighteenth European Crystallographic Meeting, Praha, Czech Republic, August 15-20, 1998. Abstracts (A), 131-132.

  • Podjarny, A.D., Lunina, N., Urzhumtsev, A.G., Vernoslova, E.A., Petrova, T. & Lunin, V. (1998). "Ab-initio phasing at 30 A of the t50S ribosomal particle with the Few Atoms Model method". ACA Annual Meeting, Arlington, Virginia, July 18-23, 1998, 11.03.08, 74.

  • Podjarny, A.D., Urzhumtsev, A.G., Vernoslova, E.A., Petrova, T., Lunina, N. & Lunin V. (1998). "Recent advances on the application of the few atom model method to the T50S ribosomal particle". Association Francaise de Cristallographie, AFC98, Orleans, 24-27 fevrier 1998, BCG-A02.

  • Urzhumtsev, A.G., Lunin, V.Y. & Lunina, N.L. (1998). "Seminvariant density decomposition and connectivity analysis in the low resolution macromolecular phasing". Eighteenth European Crystallographic Meeting, Praha, Czech Republic, August 15-20, 1998. Abstracts (A), 482-483.

  • Urzhumtseva L.M. & Urzhumtsev, A.G. (1998). "Ensemble des logiciels interactifs pour la cristallographie macromoleculaire". Association Francaise de Cristallographie, AFC98, Orleans, 24-27 fevrier 1998, BSG-A04.

  • Lunin, V.Yu., Lunina, N.L., Petrova, T.E., Urzhumtsev, A.G. & Podjarny, A.D. (1997). "A generalized likelihood and the phase cluster choice problem". In Direct methods for solving macromolecular structures, Lecture Notes, Erice, Italy, May 22 - June 02 1997, 485.

  • Lunin, V.Yu., Urzhumtsev, A.G. & Podjarny, A.D. (1997). "The solution of the low-resolution phase problem in protein crystallography". National conference on the use of X-ray, synchrotron radiations, neutrons and electrons in material studies, Dubna, 25-29 May 1997, 212. (In Russian)

  • Lunin, V.Yu., Urzhumtsev, A.G. & Podjarny, A.D. (1997). "The use of generalized likelihood based approach in low-resolution ab-initio phasing". Seventeenth European Crystallographic Meeting, Collected abstracts, Lisboa - Portugal 24/28 August 1997, 53.

  • Lunina, N.L., Lunin, V.Yu. & Urzhumtsev, A.G. (1997). "Density growing" - a new approach to local improvement of Fourier syntheses". National conference on the use of X-ray, synchrotron radiations, neutrons and electrons in material studies, Dubna, 25-29 May 1997, 222. (In Russian)

  • Lunina, N.L. & Urzhumtsev, A. (1997). "Density growing: a new approach to the local improvement of electron density maps". XVIIth European Cryst.Meeting, 24-28 August 1997, Lisbon, Portugal, 92.

  • Podjarny, A.D., Urzhumtsev, A., Tête-Favier, F., Mitschler, A., Barbanton, J., Barth, P., Urzhumtseva, L., Biellmann, J.-F., Moras, D. (1997). "The crystal structure of the complexes of aldose reductase with the inhibitors tolrestat and sorbinil". XVIIth European Cryst.Meeting, 24-28 August 1997, Lisbon, Portugal, 14.

  • Urzhumtsev, A.G., Lunin, V.Yu. & Podjarny, A.D. (1997). "Low Resolution Phasing: After First Images". Workshop "Validation and refinement of macromolecular structures", Abstracts, Porto, Portugal, August 29-30, 1997.

  • Urzhumtsev, A. & Urzhumtseva, L. (1997). "New interactive tcl/tk-based software for macromolecular crystallographers". XVIIth European Cryst.Meeting, 24-28 August 1997, Lisbon, Portugal, 184.

  • Grigera, J.R., Howard, E.I., Urzhumtsev, A.G. & Podjarny, A.D. (1996). "Hydration of biomacromolecules by multicopy molecular dynamics with diffraction constraints. Bringing into agreement diffraction and NMR data". Intern.Biophysics Congr. IUPAB, Amsterdam, the Netherlands, 1996, Coll.Abstr. P-A3-16.

  • Howard, E.I., Grigera, J.R., Podjarny, A.D. & Urzhumtsev, A.G. (1996). "Multicopy modeling of the solvent distribution in macromolecular crystals". XVII Intern.Cryst.Congr., Seattle, USA, August 8-17, 1996, Coll.Abstr., C-86.

  • Podjarny, A.D., Urzhumtsev, A.G., Howard, E.I.. & Grigera, J.R. (1996). "Modelisation multicopie de la distribution du solvant dans les cristaux macromol culaires". AFC96, 10-13 Sept. 1996, Toulouse, 42.

  • Podjarny, A.D., Urzhumtsev, A.G. & Vernoslova, E.A. (1996). "Very low resolution phasing attempts of the ribosome 50S particle from T. thermophilus by the Few Atoms Model method". XVII Intern.Cryst.Congr., Seattle, USA, August 8-17, 1996, Coll.Abstr., C-67.

  • Urzhumtsev, A.G., Podjarny, A.D., Mitschler A., Tete-Favier F., Barth P., Biellmann J.-F. & Moras D. (1996). "Etudes cristallographiques des complexes de l'aldose reductase et ses inhibiteurs". Les Cahiers IMABIO, HS, 4, 82.

  • Lunin, V.Yu., Lunina, N.L., Petrova, T.E., Vernoslova, E.A., Urzhumtsev, A.G. & Podjarny, A.D. (1995). "On the ab-initio solution of the phase problem for macromolecules at very low resolution: the Few Atoms Models method". 4th European Workshop on Crystallography of Biological Macromolecules, Como (Italy), May 21-25, O19.

  • Lunin, V.Yu., Urzhumtsev, A.G., Vernoslova, E.A., Lunina, N.L., Petrova, T.E. & Podjarny, A.D. (1995). "La methode FAM pour le phasage ab-initio: Theorie". AFC95, 24-27 Jan. 1995, Grenoble, P07a.

  • Podjarny, A.D. & Urzhumtsev, A.G. (1995). "Le remplacement moleculaire a tres basse resolution". AFC95, 24-27 Jan. 1995, Grenoble, BL08.

  • Urzhumtsev, A.G., Lunin, V.Yu., Vernoslova, E.A., Urzhumtseva, L.M. & Podjarny, A.D. (1995). "La methode FAM pour le phasage ab-initio: Applications". AFC95, 24-27 Jan. 1995, Grenoble, BL15.

  • Urzhumtsev, A.G. & Podjarny, A.D. (1995). "Very low resolution molecular replacement with envelope models". 4th European Workshop on Crystallography of Biological Macromolecules, Como (Italy), May 21-25, A04.

  • Zagari, A., Sica, F., Vitagliano, L., Scarano, G., Urzhumtsev, A.G., Podjarny, A.D. & Bocchini, V. (1995). "Cristallisation et analyse preliminaire par rayons X du facteur d'elongation hyperthermophile EF 1alpha". AFC95, 24-27 Jan. 1995, Grenoble, P43.

  • Zagari, A., Sica, F., Vitagliano, L., Scarano, G., Urzhumtsev, A.G., Podjarny, A.D. & Bocchini, V. (1995). "Crystallisation and preliminary X-ray analysis of a hyperthermophilic Archael elongation factor 1a". XXIV Congresso Nazionale, 27-29 Set. 1994, Pavia, ??

  • Lunin, V.Yu., Lunina, N.L., Petrova, T.E., Vernoslova, E.A., Urzhumtsev, A.G. & Podjarny, A.D. (1994). "A Monte Carlo Approach to low resolution phasing in protein crystallography". ACA Annual Meeting, June 25 - July 1, 1994, INFORUM, Atlanta, Georgia, Atlanta Convention Center, 178.

  • Podjarny, A.D., Urzhumtsev, A.G. & Navaza, J. (1994). "On the solution of the molecular replacement problem at very low resolution: application to a ribosome model crystal". ACA Annual Meeting, June 25 - July 1, 1994, INFORUM, Atlanta, Georgia, Atlanta Convention Center, 40.

  • Tete, F., Barth, P., Mitschler, A., Podjarny, A.D., Rondeau, J.-M., Urzhumtsev, A.G., Biellmann, J.F., Moras, D. (1994). Proceeding of the 7th Symposia on Medical Chemistry, Paris.

  • Urzhumtsev, A.G., Lunin, V.Yu., Vernoslova, E.A., Lunina, N.L., Petrova, T.E., Navaza, J. & Podjarny, A.D. (1994). "Very low resolution phasing with simple models". 15th Eur. Cryst. Meeting, Dresden, Germany, 28.8-2.9/1994, Coll.Abstr., R.Oldenbourg Verlag, Munchen, 217.

  • Urzhumtsev, A.G., Podjarny, A.D. (1993). "Enveloppes moleculaires modulees en fonction de la distance au bord". R union francophone de cristallographie de macromolecules", Ste Odile (Strasbourg), 2-5 Juin 1993, P1.

  • Podjarny, A.D., Urzhumtsev, A.G., Cavarelli, J., Rees, B., Giege, R., Thierry, J.-C. & Moras, D. (1992). "The low-resolution structure of the cubic form of the aspartyl tRNA synthetase complex: comparison of molecular replacement results and previous ab-initio low-resolution phasing". XIVth Eur. Cryst. Meeting, 2-7 August 1992, Enschede, The Netherlands, 245.

  • Urzhumtsev, A.G. (1992). "PDB models: errors in stereochemistry". XIVth Eur. Cryst. Meeting, 2-7 August 1992, Enschede, The Netherlands, 234.

  • Urzhumtsev, A.G., Podjarny,A.D., Cavarelli, J., Rees, B., Giege, R., Thierry, J.-C. & Moras, D. (1992). "Low-resolution phasing of the cubic form of the aspartyl tRNA synthetase complex confirmed by molecular replacement results". Journees Annuelles de l'Association Francaise de Cristallographie; Paris, 5-7 Mai 1992, Ministere de la Recherche et de l'Espace, II-21.

  • Lunin, V.Yu., Urzhumtsev, A.G. & Skovoroda, T.A. (1990). "Direct low-resolution phasing in protein crystallography". 16th Int.School on Crystallography, Erice, Italy, 18-29 April, 1990, Coll.Abstr.

  • Lunin, V.Yu., Urzhumtsev, A.G. & Skovoroda, T.A. (1990). "Direct low-resolution phasing in protein crystallography". Acta Cryst., A46, S, C-113.

  • Morgunova, E.Yu., Urzhumtsev, A.G., Mikhailov, A.M. & Vainstein, B.K. (1990). "The CMtV capsid protein structure at 6A resolution". Acta Cryst., A46, S, C-87-88.

  • Urzhumtsev, A.G. (1990). "Molecular bounding by two step filtration of SIR-synthesis". Acta Cryst., A46, S, C-114.

  • Chirgadze, Yu.N., Nevskaya, N.A., Urzhumtsev, A.G. & Vernoslova, E.A. (1989). "Structure refinement of "dry" form of calf lens γ-crystallin IIIb at 1.9A resolution". XIIth European Cryst. Meeting, Moscow, USSR, August 1989, Coll.Abstr., 2, 363.

  • Chirgadze, Yu.N., Vernoslova, E.A., Nikonov, S.V., Sergeev, Yu.V., Brazhnikov, E.V., Fomenkova, N.P., Lunin, V.Yu. & Urzhumtsev, A.G. (1989). "Refined structure of calf lens ?-crystalline IIIb at 2.5A resolution". XIIth European Cryst. Meeting, Moscow, USSR, August 1989, Coll.Abstr., 2, 362.

  • Urzhumtsev, A.G., Lunin, V.Yu. & Vernoslova, E.A. (1989). "FROG - new refinement program". XIIth European Cryst. Meeting, Moscow, USSR, August 1989, Coll.Abstr., 3, 193.

  • Urzhumtsev, A.G., Lunin, V.Yu. & Luzyanina, T.B. (1986). "Macromolecular position determination with a noisy synthesis at low resolution". Xth European Cryst. Meeting,Wroclaw, Poland, Coll.Abstr., 1A-01, 51-52.

  • Chirgadze, Yu.N., Nevskaya, N.A., Lunin, V.Yu. & Urzhumtsev, A.G. (1984). "Molecular structure of calf lens protein ?-crystalline at 2.7A resolution". 16-th FEBS Conference, Moscow, 1984, Coll.Abstr., 232.

  • Lunin, V.Yu. & Urzhumtsev, A.G. (1984). "Program construction for refinement of the atomic structure of macromolecules based on the fast differentiation algorithm". Acta Cryst., A40, S, C-18.

  • Lunin, V.Yu., Urzhumtsev, A.G., Chirgadze, Yu.N., Fomenkova, N.P. & Nevskaya, N.A. (1984). "Crystal structure of the calf lens protein gamma-crystalline III". Acta Cryst., A40, S, C-32.

  • Kuzin, A.P. & Urzhumtsev, A.G. (1983). "LSQ-refinement of actinoxanthin structure at 1.8A resolution". All-Union Symp. on Chemistry of Proteins and Peptides, Riga, 1983, Coll. Abstr., 186. (In Russian)

  • Fomenkova, N.P., Chirgadze, Yu.N., Sergeev, Yu.V., Nevskaya, N.A., Nikonov, S.V., Lunin, V.Yu. & Urzhumtsev, A.G. (1982). "g-crystalline structure: the pathway, domains space homology, functional groups". The First All-Union Congress on Biophysics, Moscow 1982, Coll.Abstr., 17. (In Russian)

  • Chirgadze, Yu.N., Sergeev, Yu.V., Fomenkova, N.P., Lunin, V.Yu. & Urzhumtsev, A.G. (1981). "The structure γ-crystalline IIIb from calf lens". Acta Cryst., A37, S, C-40.

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