Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

被引：375

作者：

Russel, Daniel ^{[1
]}

Lasker, Keren ^{[1
,2
]}

Webb, Ben ^{[1
]}

Velazquez-Muriel, Javier ^{[1
]}

Tjioe, Elina ^{[1
]}

Schneidman-Duhovny, Dina ^{[1
]}

Peterson, Bret ^{[3
]}

Sali, Andrej ^{[1
]}

机构：

[1] Univ Calif San Francisco, Dept Pharmaceut Chem, Dept Bioengn & Therapeut Sci, Calif Inst Quantitat Biosci QB3, San Francisco, CA 94143 USA

[2] Tel Aviv Univ, Raymond & Beverly Sackler Fac Exact Sci, Blavatnik Sch Comp Sci, IL-69978 Tel Aviv, Israel

[3] Google, Mountain View, CA USA

来源：

PLOS BIOLOGY | 2012年 / 10卷 / 01期

关键词：

MOLECULAR ARCHITECTURE; EFFICIENT; DYNAMICS; DOCKING;

D O I：

10.1371/journal.pbio.1001244

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

[No abstract available]

引用

页数：5

共 51 条

[1] PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].

Adams, Paul D. ;

Afonine, Pavel V. ;

Bunkoczi, Gabor ;

Chen, Vincent B. ;

Davis, Ian W. ;

Echols, Nathaniel ;

Headd, Jeffrey J. ;

Hung, Li-Wei ;

Kapral, Gary J. ;

Grosse-Kunstleve, Ralf W. ;

McCoy, Airlie J. ;

Moriarty, Nigel W. ;

Oeffner, Robert ;

Read, Randy J. ;

Richardson, David C. ;

Richardson, Jane S. ;

Terwilliger, Thomas C. ;

Zwart, Peter H. .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221

[2] Integrating diverse data for structure determination of macromolecular assemblies [J].

Alber, Frank ;

Foerster, Friedrich ;

Korkin, Dmitry ;

Topf, Maya ;

Sali, Andrej .

ANNUAL REVIEW OF BIOCHEMISTRY, 2008, 77 :443-477

[3] The molecular architecture of the nuclear pore complex [J].

Alber, Frank ;

Dokudovskaya, Svetlana ;

Veenhoff, Liesbeth M. ;

Zhang, Wenzhu ;

Kipper, Julia ;

Devos, Damien ;

Suprapto, Adisetyantari ;

Karni-Schmidt, Orit ;

Williams, Rosemary ;

Chait, Brian T. ;

Sali, Andrej ;

Rout, Michael P. .

NATURE, 2007, 450 (7170) :695-701

[4] Determining the architectures of macromolecular assemblies [J].

Alber, Frank ;

Dokudovskaya, Svetlana ;

Veenhoff, Liesbeth M. ;

Zhang, Wenzhu ;

Kipper, Julia ;

Devos, Damien ;

Suprapto, Adisetyantari ;

Karni-Schmidt, Orit ;

Williams, Rosemary ;

Chait, Brian T. ;

Rout, Michael P. ;

Sali, Andrej .

NATURE, 2007, 450 (7170) :683-694

[5]

[Anonymous], 2002, Molecular Modeling and Simulation

[6] Publish your computer code: it is good enough [J].

Barnes, Nick .

NATURE, 2010, 467 (7317) :753-753

[7] The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules [J].

Bau, Davide ;

Sanyal, Amartya ;

Lajoie, Bryan R. ;

Capriotti, Emidio ;

Byron, Meg ;

Lawrence, Jeanne B. ;

Dekker, Job ;

Marti-Renom, Marc A. .

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2011, 18 (01) :107-+

[8] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[9] Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT [J].

Booth, Christopher R. ;

Meyer, Anne S. ;

Cong, Yao ;

Topf, Maya ;

Sali, Andrej ;

Ludtke, Steven J. ;

Chiu, Wah ;

Frydman, Judith .

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2008, 15 (07) :746-753

[10] CHARMM: The Biomolecular Simulation Program [J].

Brooks, B. R. ;

Brooks, C. L., III ;

Mackerell, A. D., Jr. ;

Nilsson, L. ;

Petrella, R. J. ;

Roux, B. ;

Won, Y. ;

Archontis, G. ;

Bartels, C. ;

Boresch, S. ;

Caflisch, A. ;

Caves, L. ;

Cui, Q. ;

Dinner, A. R. ;

Feig, M. ;

Fischer, S. ;

Gao, J. ;

Hodoscek, M. ;

Im, W. ;

Kuczera, K. ;

Lazaridis, T. ;

Ma, J. ;

Ovchinnikov, V. ;

Paci, E. ;

Pastor, R. W. ;

Post, C. B. ;

Pu, J. Z. ;

Schaefer, M. ;

Tidor, B. ;

Venable, R. M. ;

Woodcock, H. L. ;

Wu, X. ;

Yang, W. ;

York, D. M. ;

Karplus, M. .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (10) :1545-1614

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