Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 DockAFM: benchmarking protein structures by docking under AFM topographs.

Literature DB >> 24078683

DockAFM: benchmarking protein structures by docking under AFM topographs.

Abstract

UNLABELLED: Proteins can adopt a variety of conformations. We present a simple server for scoring the agreement between 3D atomic structures and experimental envelopes obtained by atomic force microscopy. Three different structures of immunoglobulins (IgG) or blood coagulation factor V activated were tested and their agreement with several topographical surfaces was computed. This approach can be used to test structural variability within a family of proteins.
AVAILABILITY AND IMPLEMENTATION: DockAFM is available at http://biodev.cea.fr/dockafm.

Entities: Gene

Mesh：

Substances：
Immunoglobulin G
Factor V

Year: 2013 PMID： 24078683 PMCID： PMC5994945 DOI： 10.1093/bioinformatics/btt561

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

19 in total

1. High resolution AFM topographs of the Escherichia coli water channel aquaporin Z.

Authors: S Scheuring; P Ringler; M Borgnia; H Stahlberg; D J Müller; P Agre; A Engel
Journal: EMBO J Date: 1999-09-15 Impact factor: 11.598

2. Atomic force microscope.

Authors:
Journal: Phys Rev Lett Date: 1986-03-03 Impact factor: 9.161

3. Complex of linker histone H5 with the nucleosome and its implications for chromatin packing.

Authors: Li Fan; Victoria A Roberts
Journal: Proc Natl Acad Sci U S A Date: 2006-05-22 Impact factor: 11.205

Review 4. High-speed atomic force microscopy for observing dynamic biomolecular processes.

Authors: Toshio Ando; Takayuki Uchihashi; Noriyuki Kodera; Daisuke Yamamoto; Masaaki Taniguchi; Atsushi Miyagi; Hayato Yamashita
Journal: J Mol Recognit Date: 2007 Nov-Dec Impact factor: 2.137

5. High-speed atomic force microscopy: cooperative adhesion and dynamic equilibrium of junctional microdomain membrane proteins.

Authors: Adai Colom; Ignacio Casuso; Thomas Boudier; Simon Scheuring
Journal: J Mol Biol Date: 2012-07-14 Impact factor: 5.469

6. Three-dimensional model of coagulation factor Va bound to activated protein C.

Authors: J L Pellequer; A J Gale; E D Getzoff; J H Griffin
Journal: Thromb Haemost Date: 2000-11 Impact factor: 5.249

7. Conformation of ring polymers in 2D constrained environments.

Authors: G Witz; K Rechendorff; J Adamcik; G Dietler
Journal: Phys Rev Lett Date: 2011-06-15 Impact factor: 9.161

8. Super-resolution biomolecular crystallography with low-resolution data.

Authors: Gunnar F Schröder; Michael Levitt; Axel T Brunger
Journal: Nature Date: 2010-04-07 Impact factor: 49.962

9. Characterization of a factor Xa binding site on factor Va near the Arg-506 activated protein C cleavage site.

Authors: Andrew J Gale; Subramanian Yegneswaran; Xiao Xu; Jean-Luc Pellequer; John H Griffin
Journal: J Biol Chem Date: 2007-06-06 Impact factor: 5.157

10. DOT2: Macromolecular docking with improved biophysical models.

Authors: Victoria A Roberts; Elaine E Thompson; Michael E Pique; Martin S Perez; L F Ten Eyck
Journal: J Comput Chem Date: 2013-05-21 Impact factor: 3.376

4 in total

Review 1. Recent advances in RNA structurome.

Authors: Bingbing Xu; Yanda Zhu; Changchang Cao; Hao Chen; Qiongli Jin; Guangnan Li; Junfeng Ma; Siwy Ling Yang; Jieyu Zhao; Jianghui Zhu; Yiliang Ding; Xianyang Fang; Yongfeng Jin; Chun Kit Kwok; Aiming Ren; Yue Wan; Zhiye Wang; Yuanchao Xue; Huakun Zhang; Qiangfeng Cliff Zhang; Yu Zhou
Journal: Sci China Life Sci Date: 2022-06-14 Impact factor: 10.372