Automated protein model building combined with iterative structure refinement

Keywords

Computer science, Set (abstract data type), TRACE (psycholinguistics), Electron density, Resolution (logic)

References

• The Protein Data Bank: a computer-based archival file for macromolecular structures.恵子 宮北 — 1977
• Automated refinement for protein crystallography.Victor S. Lamzin, Keith S. Wilson — 1997
• Methods and applicationsHarry M. Hansen, William N. Hurwitz, William G. Madow — 1953
• [27] Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods.Eric de La Fortelle, G. Bricogne — 1997
• PHASES-95: a program package for processing and analyzing diffraction data from macromolecules.William Furey, S. Swaminathan — 1997
• Structure of a cephalosporin synthaseK. Valegård, Anke C. Terwisscha van Scheltinga, Matthew D. Lloyd — 1998
• [37] Patterson superposition and ab initio phasing.George M. Sheldrick — 1997
• Automated MAD and MIR structure solutionThomas C. Terwilliger, Joel Berendzen — 1999
• MAD phasing grows upCraig M. Ogata — 1998
• Template convolution to enhance or detect structural features in macromolecular electron-density maps.Gerard J. Kleywegt, T. Alwyn Jones — 1997
• High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.M. Hilge, Sergio M. Gloor, W. Rypniewski — 1998
• The Shake-and-Bake structure determination of triclinic lysozyme.Ashley M. Deacon, Charles M. Weeks, Russ Miller — 1998
• Improved Fourier Coefficients for Maps Using Phases from Partial Structures with ErrorsRandy J. Read — 1986
• Crystallography & NMR system: A new software suite for macromolecular structure determination.Axel T. Brünger, Paul D. Adams, G. Marius Clore — 1998
• The CCP4 suite: programs for protein crystallography.Number Collaborative Computational Project — 1994
• Assessment of phase accuracy by cross validation: the free R value. Methods and applications.Axel T. Brünger — 1993
• Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives.G. Bricogne — 1993
• Improved methods for building protein models in electron density maps and the location of errors in these models.T. Alwyn Jones, Jin-yu Zou, Sandra W. Cowan — 1991
• Towards the automatic interpretation of macromolecular electron-density maps: qualitative and quantitative matching of protein sequence to map.J.-Y. Zou, T. Alwyn Jones — 1996
• New developments in phase refinement.Jan Pieter Abrahams, RAG De Graaff — 1998

Cited by

• Structural insight into the environment of the serine/threonine protein kinase domain of titinS. Müller — 2006
• Biochemical and structural characterization of a short-chain dehydrogenase/reductase of Thermus thermophilus HB8: a hyperthermostable aldose-1-dehydrogenase with broad substrate specificity.Yukuhiko Asada, Satoshi Endo, Yukari Inoue — 2009
• An integrated approach to structural genomics.Макаренко Ольга Викторовна — 2000
• Structural Basis for Ni2+Transport and Assembly of the Urease Active Site by the Metallochaperone UreE from Bacillus pasteurii *Ricardo Lenoir — 2001
• Crystal Structure of the 47-kDa Lipoprotein of Treponema pallidum Reveals a Novel Penicillin-binding Protein*Rodolfo Bernabéu Cañete, Miguel Olmeda Fernández, Raquel Olivas — 2002
• Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27.Francisco Camacho Ferre, Eduardo Jesús Fernández Rodríguez, Manuel Martínez Camacho — 2003
• Structural Insights into Substrate Specificity and Function of Glucodextranase*Fadil Santosa, Svetlana Rudnaya — 2004
• Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans.Bautista Carrascosa, María Inmaculada — 2004
• Structure and Function of the C-terminal Domain of the Polymerase Cofactor of Rabies Virus有紀子 志村 — 2004
• Structure and activity of the atypical serine kinase Rio1N. LaRonde-LeBlanc, Tad Guszczynski, Terry Copeland — 2005
• Crystal structures of the tryptophan repressor binding protein WrbA and complexes with flavin mononucleotideR. Peretto — 2005
• Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation of the holoenzyme.Pete Pullen — 2006
• A common structural motif in the binding of virulence factors to bacterial secretion chaperones.Raphaël Couturier, Bertrand Coutourier — 2006
• Structural studies of human alkaline phosphatase in complex with strontium: Implication for its secondary effect in bonesElizabeth Kolbert — 2006
• The Zinc Finger Protein Ynr046w Is Plurifunctional and a Component of the eRF1 Methyltransferase in Yeast*Valérie Heurgué‐Hamard, Marc Graille, Nathalie Scrima — 2006
• Crystal Structure of Human Inosine TriphosphataseNeil Adkin — 2007
• Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator.José María Suñé Arbussà — 2007
• Open and Closed Structures of the UDP-glucose Pyrophosphorylase from Leishmania major*森川 潤 — 2007
• Stability for function trade-offs in the enolase superfamily "catalytic module".Rocío Zalba — 2007
• Structural Basis for the Function of DCN-1 in Protein Neddylation*Francisco Rivero Hernández — 2007

Related papers

• Simulating the behaviour of software modules by trace rewritingYabo Wang, David Lorge Parnas — 1993
• ON TRACE MOVEMENTNobuaki Nishioka — 1997
• Trace and inverse trace of Steklov eigenvalues IIYongjie Shi, Chengjie Yu — 2016
• Trace and inverse trace of Steklov eigenvalues IIYongjie Shi, Chengjie Yu — 2016
• Simulating the behaviour of software modules by trace rewritingYabo Wang, David Lorge Parnas — 1993
• Minimally resolution biased electron-density maps.Angela Altomare, Corrado Cuocci, Carmelo Giacovazzo — 2008