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Items: 1 to 20 of 84

1.

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.

Segura J, Sanchez-Garcia R, Tabas-Madrid D, Cuenca-Alba J, Sorzano CO, Carazo JM.

Biophys J. 2016 Feb 23;110(4):766-75. doi: 10.1016/j.bpj.2015.11.3519. Epub 2016 Jan 7.

2.

Modeling, docking, and fitting of atomic structures to 3D maps from cryo-electron microscopy.

Allen GS, Stokes DL.

Methods Mol Biol. 2013;955:229-41. doi: 10.1007/978-1-62703-176-9_13.

3.

Computational methods for constructing protein structure models from 3D electron microscopy maps.

Esquivel-Rodríguez J, Kihara D.

J Struct Biol. 2013 Oct;184(1):93-102. doi: 10.1016/j.jsb.2013.06.008. Epub 2013 Jun 21.

4.

Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.

Esquivel-Rodríguez J, Kihara D.

J Phys Chem B. 2012 Jun 14;116(23):6854-61. doi: 10.1021/jp212612t. Epub 2012 Mar 30.

5.

Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.

de Vries SJ, Chauvot de Beauchêne I, Schindler CE, Zacharias M.

Biophys J. 2016 Feb 23;110(4):785-97. doi: 10.1016/j.bpj.2015.12.038. Epub 2016 Feb 1.

7.

Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies.

Velazquez-Muriel JA, Valle M, Santamaría-Pang A, Kakadiaris IA, Carazo JM.

Structure. 2006 Jul;14(7):1115-26.

8.

Navigating 3D electron microscopy maps with EM-SURFER.

Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D.

BMC Bioinformatics. 2015 May 30;16:181. doi: 10.1186/s12859-015-0580-6.

9.

Classification and Exploration of 3D Protein Domain Interactions Using Kbdock.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Methods Mol Biol. 2016;1415:91-105. doi: 10.1007/978-1-4939-3572-7_5.

PMID:
27115629
10.

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage.

Garzón JI, Kovacs J, Abagyan R, Chacón P.

Bioinformatics. 2007 Feb 15;23(4):427-33. Epub 2006 Dec 6.

PMID:
17150992
11.

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement.

Jackson RN, McCoy AJ, Terwilliger TC, Read RJ, Wiedenheft B.

Nat Protoc. 2015 Sep;10(9):1275-84. doi: 10.1038/nprot.2015.069. Epub 2015 Jul 30.

12.

SPI-EM: towards a tool for predicting CATH superfamilies in 3D-EM maps.

Velázquez-Muriel JA, Sorzano CO, Scheres SH, Carazo JM.

J Mol Biol. 2005 Jan 28;345(4):759-71.

PMID:
15588824
13.

Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement.

Zhu J, Cheng L, Fang Q, Zhou ZH, Honig B.

J Mol Biol. 2010 Apr 2;397(3):835-51. doi: 10.1016/j.jmb.2010.01.041. Epub 2010 Jan 28.

14.

FEMME database: topologic and geometric information of macromolecules.

Jiménez-Lozano N, Chagoyen M, Cuenca-Alba J, Carazo JM.

J Struct Biol. 2003 Oct-Nov;144(1-2):104-13.

PMID:
14643213
15.

iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates.

Lopéz-Blanco JR, Chacón P.

J Struct Biol. 2013 Nov;184(2):261-70. doi: 10.1016/j.jsb.2013.08.010. Epub 2013 Aug 30.

PMID:
23999189
16.

Emerging issues of connexin channels: biophysics fills the gap.

Harris AL.

Q Rev Biophys. 2001 Aug;34(3):325-472. Review. Erratum in: Q Rev Biophys 2002 Feb;35(1):109.

PMID:
11838236
17.

Flexible fitting in 3D-EM with incomplete data on superfamily variability.

Velazquez-Muriel JA, Carazo JM.

J Struct Biol. 2007 May;158(2):165-81. Epub 2006 Oct 24.

PMID:
17257856
18.

3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.

Nogales-Cadenas R, Jonic S, Tama F, Arteni AA, Tabas-Madrid D, Vázquez M, Pascual-Montano A, Sorzano CO.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W363-7. doi: 10.1093/nar/gkt385. Epub 2013 May 13.

19.
20.

DNA binding alters coactivator interaction surfaces of the intact VDR-RXR complex.

Zhang J, Chalmers MJ, Stayrook KR, Burris LL, Wang Y, Busby SA, Pascal BD, Garcia-Ordonez RD, Bruning JB, Istrate MA, Kojetin DJ, Dodge JA, Burris TP, Griffin PR.

Nat Struct Mol Biol. 2011 May;18(5):556-63. doi: 10.1038/nsmb.2046. Epub 2011 Apr 10.

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