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 UCSF Chimera, MODELLER, and IMP: an integrated modeling system.

Literature DB >> 21963794

UCSF Chimera, MODELLER, and IMP: an integrated modeling system.

Zheng Yang¹, Keren Lasker, Dina Schneidman-Duhovny, Ben Webb, Conrad C Huang, Eric F Pettersen, Thomas D Goddard, Elaine C Meng, Andrej Sali, Thomas E Ferrin.

Abstract

Structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. Here we present the integration of several modeling tools into UCSF Chimera. These include comparative modeling by MODELLER, simultaneous fitting of multiple components into electron microscopy density maps by IMP MultiFit, computing of small-angle X-ray scattering profiles and fitting of the corresponding experimental profile by IMP FoXS, and assessment of amino acid sidechain conformations based on rotamer probabilities and local interactions by Chimera.

Entities: CellLine Chemical Disease Gene Species

Mesh：

Substances：

Year: 2011 PMID： 21963794 PMCID： PMC3410985 DOI： 10.1016/j.jsb.2011.09.006

Source DB: PubMed Journal: J Struct Biol ISSN： 1047-8477 Impact factor: 2.867

57 in total

1. The penultimate rotamer library.

Authors: S C Lovell; J M Word; J S Richardson; D C Richardson
Journal: Proteins Date: 2000-08-15

2. ATP-bound states of GroEL captured by cryo-electron microscopy.

Authors: N A Ranson; G W Farr; A M Roseman; B Gowen; W A Fenton; A L Horwich; H R Saibil
Journal: Cell Date: 2001-12-28 Impact factor: 41.582

3. On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation.

Authors: J Navaza; J Lepault; F A Rey; C Alvarez-Rúa; J Borge
Journal: Acta Crystallogr D Biol Crystallogr Date: 2002-09-28

Review 4. The universally conserved GroE (Hsp60) chaperonins.

Authors: J Zeilstra-Ryalls; O Fayet; C Georgopoulos
Journal: Annu Rev Microbiol Date: 1991 Impact factor: 15.500

5. structureViz: linking Cytoscape and UCSF Chimera.

Authors: John H Morris; Conrad C Huang; Patricia C Babbitt; Thomas E Ferrin
Journal: Bioinformatics Date: 2007-07-10 Impact factor: 6.937

6. How well can the accuracy of comparative protein structure models be predicted?

Authors: David Eramian; Narayanan Eswar; Min-Yi Shen; Andrej Sali
Journal: Protein Sci Date: 2008-10-01 Impact factor: 6.725

7. The complete genome sequence of Escherichia coli K-12.

Authors: F R Blattner; G Plunkett; C A Bloch; N T Perna; V Burland; M Riley; J Collado-Vides; J D Glasner; C K Rode; G F Mayhew; J Gregor; N W Davis; H A Kirkpatrick; M A Goeden; D J Rose; B Mau; Y Shao
Journal: Science Date: 1997-09-05 Impact factor: 47.728

8. Homologous plant and bacterial proteins chaperone oligomeric protein assembly.

Authors: S M Hemmingsen; C Woolford; S M van der Vies; K Tilly; D T Dennis; C P Georgopoulos; R W Hendrix; R J Ellis
Journal: Nature Date: 1988-05-26 Impact factor: 49.962

9. FoXS: a web server for rapid computation and fitting of SAXS profiles.

Authors: Dina Schneidman-Duhovny; Michal Hammel; Andrej Sali
Journal: Nucleic Acids Res Date: 2010-05-27 Impact factor: 16.971

10. ModBase, a database of annotated comparative protein structure models, and associated resources.

Authors: Ursula Pieper; Benjamin M Webb; David T Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C Meng; Eric F Pettersen; Conrad C Huang; Ruchira S Datta; Parthasarathy Sampathkumar; Mallur S Madhusudhan; Kimmen Sjölander; Thomas E Ferrin; Stephen K Burley; Andrej Sali
Journal: Nucleic Acids Res Date: 2010-11-19 Impact factor: 16.971

207 in total

1. Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification.

Authors: Matthew M Makowski; Esther Willems; Pascal W T C Jansen; Michiel Vermeulen
Journal: Mol Cell Proteomics Date: 2015-11-11 Impact factor: 5.911

2. Stability engineering of anti-EGFR scFv antibodies by rational design of a lambda-to-kappa swap of the VL framework using a structure-guided approach.

Authors: Andreas Lehmann; Josephine H F Wixted; Maxim V Shapovalov; Heinrich Roder; Roland L Dunbrack; Matthew K Robinson
Journal: MAbs Date: 2015-09-04 Impact factor: 5.857

UCSF Chimera, MODELLER, and IMP: an integrated modeling system.

1. The penultimate rotamer library.

2. ATP-bound states of GroEL captured by cryo-electron microscopy.

3. On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation.

Review 4. The universally conserved GroE (Hsp60) chaperonins.

5. structureViz: linking Cytoscape and UCSF Chimera.

6. How well can the accuracy of comparative protein structure models be predicted?

7. The complete genome sequence of Escherichia coli K-12.

8. Homologous plant and bacterial proteins chaperone oligomeric protein assembly.

9. FoXS: a web server for rapid computation and fitting of SAXS profiles.

10. ModBase, a database of annotated comparative protein structure models, and associated resources.

1. Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification.

2. Stability engineering of anti-EGFR scFv antibodies by rational design of a lambda-to-kappa swap of the VL framework using a structure-guided approach.

3. A novel TIMP3 mutation associated with a retinitis pigmentosa-like phenotype.

4. Further evidence for the likely completeness of the library of solved single domain protein structures.

5. Variability of Protein Structure Models from Electron Microscopy.

6. Accurate SAXS profile computation and its assessment by contrast variation experiments.

7. Mapping Antigenic Epitopes on the Human Bocavirus Capsid.

Review 8. Redox Systems Biology: Harnessing the Sentinels of the Cysteine Redoxome.

9. Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins.

10. Experimental charge density from electron microscopic maps.