• Gorgon and pathwalking: macrom...

Treffer: Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps.

Title:
Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps.
Authors:
Baker ML; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA. mbaker@bcm.edu, Baker MR, Hryc CF, Ju T, Chiu W
Source:
Biopolymers [Biopolymers] 2012 Sep; Vol. 97 (9), pp. 655-68.
Publication Type:
Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
Language:
English
Journal Info:
Publisher: Wiley Country of Publication: United States NLM ID: 0372525 Publication Model: Print Cited Medium: Print ISSN: 0006-3525 (Print) Linking ISSN: 00063525 NLM ISO Abbreviation: Biopolymers Subsets: MEDLINE
Imprint Name(s):
Original Publication: New York, NY : Wiley
MeSH Terms:
Models, Molecular*, Cryoelectron Microscopy/*methods , Proteins/*chemistry, Nanotechnology ; Protein Structure, Secondary
References:
Cell. 1992 Feb 7;68(3):415-20. (PMID: 1531448)
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W24-8. (PMID: 21602266)
J Struct Biol. 2006 Sep;155(3):470-81. (PMID: 16762565)
Nature. 2003 Jun 26;423(6943):949-55. (PMID: 12827192)
Nat Protoc. 2010 Sep;5(10):1697-708. (PMID: 20885381)
Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1002-11. (PMID: 16929101)
Structure. 2008 Mar;16(3):441-8. (PMID: 18334219)
Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1355-60. (PMID: 21220301)
Trends Cell Biol. 2006 Mar;16(3):144-50. (PMID: 16459078)
J Mol Biol. 2010 Apr 2;397(3):835-51. (PMID: 20109465)
J Mol Biol. 2003 Sep 12;332(2):399-413. (PMID: 12948490)
Nature. 2008 May 15;453(7193):415-9. (PMID: 18449192)
J Mol Biol. 2006 Apr 14;357(5):1655-68. (PMID: 16490207)
Structure. 2007 Jan;15(1):7-19. (PMID: 17223528)
J Mol Biol. 2004 May 21;339(1):117-30. (PMID: 15123425)
Trends Biochem Sci. 2000 Dec;25(12):624-31. (PMID: 11116190)
PLoS Comput Biol. 2006 Oct 27;2(10):e146. (PMID: 17069457)
J Struct Biol. 2007 Jan;157(1):38-46. (PMID: 16859925)
Comput Graph Forum. 2010;29(7):2243-2252. (PMID: 21124809)
Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):4967-72. (PMID: 20194787)
Curr Opin Struct Biol. 2008 Apr;18(2):218-28. (PMID: 18403197)
J Struct Biol. 1999 Dec 1;128(1):82-97. (PMID: 10600563)
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W197-201. (PMID: 18463136)
Nat Struct Mol Biol. 2006 Feb;13(2):147-52. (PMID: 16429154)
J Mol Biol. 2009 Sep 11;392(1):181-90. (PMID: 19596339)
J Comput Chem. 2004 Oct;25(13):1605-12. (PMID: 15264254)
J Struct Biol. 2011 May;174(2):360-73. (PMID: 21296162)
J Struct Biol. 2004 Aug;147(2):116-27. (PMID: 15193640)
Methods Enzymol. 2010;483:1-29. (PMID: 20888467)
Bioinformatics. 2000 Apr;16(4):404-5. (PMID: 10869041)
Science. 2010 Aug 27;329(5995):1038-43. (PMID: 20798312)
J Struct Biol. 2005 Feb;149(2):191-203. (PMID: 15681235)
Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10644-8. (PMID: 19487668)
J Mol Biol. 2001 May 18;308(5):1033-44. (PMID: 11352589)
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2240-9. (PMID: 15572777)
Biopolymers. 2003 Feb;68(2):223-33. (PMID: 12548625)
J Mol Biol. 2007 Aug 17;371(3):812-35. (PMID: 17585939)
Structure. 2005 Mar;13(3):355-62. (PMID: 15766536)
Comput Aided Des. 2007 May;39(5):352-360. (PMID: 18449328)
J Struct Biol. 2010 Aug;171(2):216-22. (PMID: 20353825)
EMBO J. 2009 Mar 18;28(6):755-65. (PMID: 19229291)
J Mol Biol. 1997 Oct 24;273(2):371-6. (PMID: 9344745)
Methods Enzymol. 2010;483:47-72. (PMID: 20888469)
Structure. 2003 Sep;11(9):1043-7. (PMID: 12962622)
Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9. (PMID: 2025413)
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2222-9. (PMID: 15572775)
Cell. 2010 Apr 30;141(3):472-82. (PMID: 20398923)
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501. (PMID: 20383002)
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2115-25. (PMID: 15572764)
Structure. 2012 Mar 7;20(3):450-63. (PMID: 22405004)
J Mol Biol. 2010 Apr 2;397(3):852-63. (PMID: 20036256)
Methods Enzymol. 1997;277:173-208. (PMID: 18488310)
Nature. 2010 Jan 21;463(7279):379-83. (PMID: 20090755)
EMBO J. 2010 May 19;29(10):1652-8. (PMID: 20389283)
Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9610-5. (PMID: 18621707)
Cell. 2001 Dec 28;107(7):869-79. (PMID: 11779463)
Nat Struct Mol Biol. 2010 Jul;17(7):830-6. (PMID: 20543830)
EMBO J. 1986 Apr;5(4):819-22. (PMID: 3709525)
Nature. 2008 Feb 28;451(7182):1130-4. (PMID: 18305544)
J Struct Biol. 2009 Jan;165(1):1-9. (PMID: 18926912)
EMBO J. 2011 Aug 09;30(18):3854-63. (PMID: 21829169)
Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1867-72. (PMID: 18238898)
Cell. 1998 Feb 6;92(3):291-4. (PMID: 9476889)
Grant Information:
P41RR002250 United States RR NCRR NIH HHS; R01 GM079429 United States GM NIGMS NIH HHS; T15LM007093 United States LM NLM NIH HHS; P41 RR002250 United States RR NCRR NIH HHS; R01GM079429 United States GM NIGMS NIH HHS; T15 LM007093 United States LM NLM NIH HHS
Substance Nomenclature:
0 (Proteins)
Entry Date(s):
Date Created: 20120615 Date Completed: 20120821 Latest Revision: 20240318
Update Code:
20250114
PubMed Central ID:
PMC3899894
DOI:
10.1002/bip.22065
PMID:
22696403
Database:
MEDLINE

Weitere Informationen

The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10 Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo-EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid-body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions.
(Copyright © 2012 Wiley Periodicals, Inc.)