DOI: 10.1016/j.str.2006.05.013. Flexible Fitting in 3D-EM Guided by the Structural Variability of Protein Superfamilies

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

10.1016/j.str.2006.05.013

Crossref journal-article

Elsevier BV

Structure (78)

Bibliography

Velazquez-Muriel, J.-Ã., Valle, M., SantamarÃa-Pang, A., Kakadiaris, I. A., & Carazo, J.-M. (2006). Flexible Fitting in 3D-EM Guided by the Structural Variability of Protein Superfamilies. Structure, 14(7), 1115â1126.

Authors 5

Javier-Ángel Velazquez-Muriel (first)
Mikel Valle (additional)
Alberto Santamaría-Pang (additional)
Ioannis A. Kakadiaris (additional)
José-María Carazo (additional)

References 29 Referenced 40

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10.1110/ps.0242703 / Protein Sci. / Cyclic coordinate descent: a robotics algorithm for protein loop closure by Canutescu (2003)
10.1006/jmbi.2002.5438 / J. Mol. Biol. / Multi-resolution contour-based fitting of macromolecular structures by Chacon (2002)
10.1016/j.jsb.2003.09.008 / J. Struct. Biol. / Low-resolution structure refinement in electron microscopy by Chen (2003)
10.1002/j.1460-2075.1994.tb06676.x / EMBO J. / Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus by Evarsson (1994)
10.1016/j.str.2005.01.007 / Structure / Fitting of high-resolution structures into electron microscopy reconstruction images by Fabiola (2005)
10.1016/0263-7855(96)00018-5 / J. Mol. Graph. / VMD: visual molecular dynamics by Humphrey (1996)
10.1006/jmbi.2001.4633 / J. Mol. Biol. / Bridging the information gap: computational tools for intermediate resolution structure interpretation by Jiang (2001)
10.1107/S0108767390010224 / Acta Crystallogr. A / Improved methods for building protein models in electron density maps and the location of errors in these models by Jones (1991)
10.1107/S0108767388010128 / Acta Crystallogr. A / On the orthogonal transformation used for structural comparisons by Kearsley (1989)
10.1107/S0907444903011247 / Acta Crystallogr. D Biol. Crystallogr. / Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom by Kovacs (2003)
10.1006/jmbi.2000.4168 / J. Mol. Biol. / Structure of a mutant EF-G reveals domain III and possibly the fusidic acid binding site by Laurberg (2000)
10.1107/S090744499801405X / Acta Crystallogr. D Biol. Crystallogr. / Efficient anisotropic refinement of macromolecular structures using FFT by Murshudov (1999)
10.1016/S0022-2836(05)80134-2 / J. Mol. Biol. / SCOP: a structural classification of proteins database for the investigation of sequences and structures by Murzin (1995)
10.1002/0471721204.ch13 / Methods Biochem. Anal. / The CATH domain structure database by Orengo (2003)
10.1110/ps.0215902 / Protein Sci. / MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison by Ortiz (2002)
10.1002/jcc.20084 / J. Comput. Chem. / UCSF Chimera—a visualization system for exploratory research and analysis by Pettersen (2004)
{'key': '10.1016/j.str.2006.05.013_bib18', 'series-title': 'Numerical Recipes in C', 'author': 'Press', 'year': '1988'} / Numerical Recipes in C by Press (1988)
10.1073/pnas.0404703101 / Proc. Natl. Acad. Sci. USA / Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation by Qian (2004)
10.1107/S0907444900009562 / Acta Crystallogr. D Biol. Crystallogr. / Fitting atomic models into electron-microscopy maps by Rossmann (2000)
10.1016/j.jmb.2004.01.048 / J. Mol. Biol. / Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis by Tama (2004)
10.1016/j.sbi.2005.08.001 / Curr. Opin. Struct. Biol. / Combining electron microscopy and comparative protein structure modeling by Topf (2005)
10.1016/j.jsb.2004.11.004 / J. Struct. Biol. / Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy by Topf (2005)
10.1016/j.jmb.2006.01.062 / J. Mol. Biol. / Refinement of protein structures by iterative comparative modeling and cryoEM density fitting by Topf (2006)
10.1016/S0092-8674(03)00476-8 / Cell / Locking and unlocking of ribosomal motions by Valle (2003)
10.1016/j.jmb.2004.11.005 / J. Mol. Biol. / SPI-EM: towards a tool for predicting CATH superfamilies in 3D-EM maps by Velazquez-Muriel (2005)
10.1006/jsbi.1998.4074 / J. Struct. Biol. / Quantitative fitting of atomic models into observed densities derived by electron microscopy by Volkmann (1999)
10.1016/S0092-8674(00)80905-8 / Cell / Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing by Wilson (1998)
10.1006/jsbi.2000.4350 / J. Struct. Biol. / Using situs for flexible and rigid-body fitting of multiresolution single-molecule data by Wriggers (2001)

Dates

Type	When
Created	19 years, 1 month ago (July 19, 2006, 11:01 a.m.)
Deposited	1 year, 6 months ago (Feb. 5, 2024, 7:19 a.m.)
Indexed	1 year ago (Aug. 12, 2024, 9:15 a.m.)
Issued	19 years, 2 months ago (July 1, 2006)
Published	19 years, 2 months ago (July 1, 2006)
Published Print	19 years, 2 months ago (July 1, 2006)

Funders 0

None

BibTeX

@article{Velazquez_Muriel_2006, title={Flexible Fitting in 3D-EM Guided by the Structural Variability of Protein Superfamilies}, volume={14}, ISSN={0969-2126}, url={http://dx.doi.org/10.1016/j.str.2006.05.013}, DOI={10.1016/j.str.2006.05.013}, number={7}, journal={Structure}, publisher={Elsevier BV}, author={Velazquez-Muriel, Javier-Ángel and Valle, Mikel and Santamaría-Pang, Alberto and Kakadiaris, Ioannis A. and Carazo, José-María}, year={2006}, month=jul, pages={1115–1126} }

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