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Flexible Fitting in 3D-EM Guided by the Structural Variability of Protein Superfamilies

Javier-Ángel Velazquez-Muriel, Mikel Valle, Alberto Santamaría-Pang, Ioannis A. Kakadiaris, José-María Carazo
2006 Structure  
A method for flexible fitting of molecular models into three-dimensional electron microscopy (3D-EM) reconstructions at a resolution range of 8-12 Å is proposed.  ...  A structural alignment of domains belonging to the superfamily, followed by a principal components analysis, is performed, and the first three principal components of the decomposition are explored.  ...  We assume that the superfamily corresponding to the domain present in the 3D-EM map is known, either by sequence comparison or by using rigid body fitting (Velazquez-Muriel et al., 2005) .  ... 
doi:10.1016/j.str.2006.05.013 pmid:16843893 fatcat:hcd7h2ul5fafxemomotis2dal4

Comparison of molecular dynamics and superfamily spaces of protein domain deformation

Javier A Velazquez-Muriel, Manuel Rueda, Isabel Cuesta, Alberto Pascual-Montano, Modesto Orozco, Jose-Maria Carazo
2009 BMC Structural Biology  
Also, the SF-space does not sample all possibilities offered by the MD-space, but often introduces very large changes along just a few deformation modes, whose number tend to a plateau as the number of  ...  Second, that conformational changes from variation in a superfamily are larger and much simpler than those allowed by physical deformability.  ...  complexes, and variation along domains in a superfamily is a good way of obtaining that information.  ... 
doi:10.1186/1472-6807-9-6 pmid:19220918 pmcid:PMC2666742 fatcat:pyxql5smdre2nid2vhbey5iy7u

Structure–function mapping of a heptameric module in the nuclear pore complex

Javier Fernandez-Martinez, Jeremy Phillips, Matthew D. Sekedat, Ruben Diaz-Avalos, Javier Velazquez-Muriel, Josef D. Franke, Rosemary Williams, David L. Stokes, Brian T. Chait, Andrej Sali, Michael P. Rout
2012 Journal of Cell Biology  
(15 Å).  ...  In this stage, a Monte Carlo move consisted of either a two-degree rotation or 5-Å translation at a temperature of 273°C.  ... 
doi:10.1083/jcb.201109008 pmid:22331846 pmcid:PMC3283990 fatcat:hu2naaexrffcpddvbziupxxxlu

Quasi-Atomic Model of Bacteriophage T7 Procapsid Shell: Insights into the Structure and Evolution of a Basic Fold

Xabier Agirrezabala, Javier A. Velázquez-Muriel, Paulino Gómez-Puertas, Sjors H.W. Scheres, José M. Carazo, José L. Carrascosa
2007 Structure  
The procapsid structure at 10 Å resolution was used to obtain a quasi-atomic model by fitting a homology model of the T7 capsid protein gp10 that was based on the atomic structure of the HK97 capsid protein  ...  A number of fold similarities, such as the fitting of domains A and P into the L-shaped procapsid subunit, are evident between both viral systems.  ...  : the thick procapsid shell (50 Å ) is transformed into a much thinner shell (25 Å ), which is accomplished by a significant rearrangement of the major shell subunit interactions.  ... 
doi:10.1016/j.str.2007.03.004 pmid:17437718 fatcat:wknfnb2mdrcexemwnyvjtyzwva

Molecular Rearrangements Involved in the Capsid Shell Maturation of Bacteriophage T7

Alina Ionel, Javier A. Velázquez-Muriel, Daniel Luque, Ana Cuervo, José R. Castón, José M. Valpuesta, Jaime Martín-Benito, José L. Carrascosa
2010 Journal of Biological Chemistry  
a host under challenging environmental conditions.  ...  The rearrangements include tilting, in-plane rotation, and radial expansion of the subunits, as well as a relative bending of the A-and P-domains of each subunit.  ...  We are grateful to Ron Conway, Mike Homer, Intel, Hewlett-Packard, IBM, and Netapp for computer hardware gifts to A. Sali.  ... 
doi:10.1074/jbc.m110.187211 pmid:20962334 pmcid:PMC3012979 fatcat:itqhfneyw5hxjfancvep3att6m

A method for integrative structure determination of protein-protein complexes

Dina Schneidman-Duhovny, Andrea Rossi, Agustin Avila-Sakar, Seung Joong Kim, Javier Velázquez-Muriel, Pavel Strop, Hong Liang, Kristin A. Krukenberg, Maofu Liao, Ho Min Kim, Solmaz Sobhanifar, Volker Dötsch (+5 others)
2012 Computer applications in the biosciences : CABIOS  
Results: Here, we present a combined approach that computationally integrates data from a variety of fast and accessible experimental techniques for rapid and accurate structure determination of protein-protein  ...  The method is tested on a docking benchmark consisting of 176 known complex structures and simulated experimental data.  ...  ACKNOWLEDGEMENTS We wish to thank Javier Chaparro-Riggers for engineering J16 Fab and Michael Chin for the PCSK9 and J16 Fab samples.  ... 
doi:10.1093/bioinformatics/bts628 pmid:23093611 pmcid:PMC3519461 fatcat:ck4vkfpaezcgtef4nfhbnwcfgu

The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

Shruthi Viswanath, Massimiliano Bonomi, Seung Joong Kim, Vadim A. Klenchin, Keenan C. Taylor, King C. Yabut, Neil T. Umbreit, Heather A. Van Epps, Janet Meehl, Michele H. Jones, Daniel Russel, Javier A. Velazquez-Muriel (+6 others)
2017 Molecular Biology of the Cell  
The model led to the identification of a single, essential heptad in the coiled-coil of Spc110 and a minimal PACT domain. It also led to a proposed pathway for the integration of Spc110 into the SPB.  ...  The model is validated by several methods that include a genetic analysis of the conserved PACT domain that recruits Spc110, a protein related to pericentrin, to the SPB.  ...  In addition, the distance between the IL2 and CP was only defined to have a maximum of 300 Å with a minimum of 0 Å.  ... 
doi:10.1091/mbc.e17-06-0397 pmid:28814505 pmcid:PMC5687031 fatcat:a6aduooagbduzf57nkrowobvna

Reescribir el Vértigo (De entre los vivos): la impronta cinematográfica de Hitchcock en "Así empieza lo malo", de Javier Marías

Carmen María López López
2017 Signa Revista de la Asociación Española de Semiótica  
Javier Marías. Así empieza lo malo.  ...  From a semiotic perspective, it is essential to focus our attention on the concept of transduction of fictional worlds (Dolezel, 1999) , with the aim of establishing the links between the literary work  ...  HITCHCOCK EN ASÍ EMPEIZA LO MALO, DE JAVIER MARÍAS Esta idea que se enuncia a propósito de La ventana indiscreta, se hace extensible a Vértigo y a la narrativa de Javier Marías.  ... 
doi:10.5944/signa.vol26.2017.19956 fatcat:xmla4zz4obdrvf6puloygethaa

La écfrasis en la obra de Luis Javier Moreno

Natalia Carbajosa Palmero
2013 Signa Revista de la Asociación Española de Semiótica  
los poemas elegidos para el análisis.The present article analyzes the ekphrastic poetry of Luis Javier Moreno within the theoretical and historical context of exphrasis as a primordial semiotic and epistemological  ...  source; furthermore, as a mediating element between the poem and reality.  ...  -similar al que, explícitamente, Velázquez llevó a cabo en «Las Meninas».  ... 
doi:10.5944/signa.vol22.2013.6350 fatcat:bsdteesqfzhorbjolnl7c6kw2y

Page 5430 of Mathematical Reviews Vol. , Issue 2002H [page]

2002 Mathematical Reviews  
Velazquez [Luis Velazquez], Semiorthogonal functions and quadrature formulas (Spanish) (141-150); Ricardo Celorrio, Victor Dominguez and Francisco-Javier Sayas, Asymptotics of finite element Lagrange interpolation  ...  Almira, Muntz theorems on Besov spaces and on C*[{a,b] (53-60); Mohamed Amara, Héléne Barucq and Muriel Duloué, Une formulation convergente des équations de Navier-Stokes tridimensionnelles [A convergent  ... 

Índice general de Estudios de Historia Novohispana, números 1 al l5

Juan Domingo Vidargas del Moral
2009 Estudios de Historia Novohispana  
La primera editora responsable fue la doctora Josefina Muriel. Al año siguiente fue auxiliada por Rosa Camelo quien en números posteriores fungió como editora.  ...  Se pretendía dar a conocer ensayos y artículos, resultados muchas veces de trabajos más extensos, que contribuyeran al conocimiento de la historia colonial de México.  ...  ÍNDICE GENERAL DE ESTUDIOS DE HISTORIA NOVOHISPANA VOLÚMENES 1 A 15 ductivos investigadores.  ... 
doi:10.22201/iih.24486922e.1996.016.3431 fatcat:fmiysuufyrctnfbmggavdq4mwm

Leonardo, Richard (editor) Poéticas de lo negro. Literatura y otros discursos acerca de lo afroperuano en el siglo XX. Lima, Hipocampo Editores, 2013; 190 pp

Juan Manuel Olaya Rocha
2015 Letras : Órgano de la Facultad de Letras y Ciencias Humanas  
Asimismo, entre los nacionales cabe destacar a Richard Leonardo, Víctor Quiroz, Judith Paredes, Margarita Saona, así como a Isabel Polo, Yesabeth Muriel y Gabriela Javier Caballero, quienes contribuyen  ...  llena un espacio que aún está por desentrañarse, continuando así con los aportes sobre lo afroperuano en la literatura que se han ido sucediendo en los últimos años de parte de investigadores como Marcel Velázquez  ... 
doaj:d6d2571d6f824b6da10a5cbbd6264925 fatcat:ya3ko7vdbrh53dqxszm4dzjp5i

Studying interactions between vaccinia virus protein a46 and the cellular protein MyD88

S. Fedosyuk, T. Skern
2011 Acta Crystallographica Section A Foundations of Crystallography  
Velázquez-Muriel, b Daniel Luque, a Ana Cuervo, a José R. Caston, a José M. Valpuesta, a Jaime Martín-Benito, a José L.  ...  E-mail: Acta Cryst. (2011) A67, C414 Reorganization of the shell protein during the maturation of bacteriophage T7 Alina Ionel, a Javier A.  ...  A result of this disorder is strong layers of diffuse scattering perpendicular to the channel axis at one-third increments between the average 'Bragg' Layer lines.  ... 
doi:10.1107/s0108767311089628 fatcat:5erj646q5ra45crmdmeiglytzy

Antonio Benavides Castillo y Ricardo Armijo Torres (eds.), Prácticas funerarias y arquitectura en tiempo y espacio

María Del Rosario Domínguez Carrasco
2015 Estudios de Cultura Maya  
Alejandro Tovalín Ahumada, José Adolfo Velázquez de León Collins y Javier Montes de Paz nos ofrecen importantes datos a través del trabajo titulado "Tres tumbas en la Acrópolis de Bonampak, Chiapas, México  ...  El libro cierra con el trabajo de María José Con Uribe y Mónica López Portillo Guzmán, dedicado a Alejandro Martínez Muriel, que lleva por título "El Castillo de Tulum: Historia de un edificio".  ... 
doi:10.19130/iifl.ecm.2016.47.749 fatcat:xf3g2cvhb5gzlash2jzu6rzpcq

Tolède vue par les chroniqueurs Rodrigo Jiménez de Rada et Pero López de Ayala, rapprochés de leurs prédécesseurs, de langue arabe, latine ou romane

Jean-Pierre Molénat
2014 Mélanges de la Casa de Velázquez  
Molénat, Jean-Pierre (2013), « Les noms des mudéjars revisités à partir de Tolède et du Portugal », dans Christian Müller et Muriel Roiland-Rouabah, Les non-dits du nom.  ...  Gorosterratzu, Javier (1925), Don Rodrigo Jiménez de Rada, gran estadista, escritor y prelado , Pampelune.  ... 
doi:10.4000/mcv.5563 fatcat:j5ax6wuhzfbcdnnnran2fqihgq
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