Community-wide assessment of protein-interface modeling suggests improvements to design methodology

Journal of Molecular Biology

Volumn 414, Issue 2, 2011, Pages 289-302

  Fleishman, Sarel J ^a,w   Whitehead, Timothy A ^a   Strauch, Eva Maria ^a   Corn, Jacob E ^a,ap   Qin, Sanbo ^b   Zhou, Huan Xiang ^b   Mitchell, Julie C ^c   Demerdash, Omar N A ^c   Takeda Shitaka, Mayuko ^d   Terashi, Genki ^d   Moal, Iain H ^e   Li, Xiaofan ^e   Bates, Paul A ^e   Zacharias, Martin ^f   Park, Hahnbeom ^g   Ko, Jun Su ^g   Lee, Hasup ^g   Seok, Chaok ^g   Bourquard, Thomas ^h,i,j   Bernauer, Julie ⁱ   Poupon, Anne ^k,l,m   Azé, Jérôme ⁱ   Soner, Seren ⁿ   Ovali, Şefik Kerem ⁿ   Ozbek, Pemra ⁿ   Tal, Nir Ben ^o   Haliloglu, Türkan ⁿ   Hwang, Howook ^p   Vreven, Thom ^p   Pierce, Brian G ^p   Weng, Zhiping ^p   Pérez Cano, Laura ^q   Pons, Carles ^q   Fernández Recio, Juan ^q   Jiang, Fan ^r   Yang, Feng ^s   Gong, Xinqi ^s   Cao, Libin ^s   Xu, Xianjin ^s   Liu, Bin ^s   Wang, Panwen ^s   Li, Chunhua ^s   Wang, Cunxin ^s   Robert, Charles H ^t   Guharoy, Mainak ^t   Liu, Shiyong ^u   Huang, Yangyu ^u   Li, Lin ^u   Guo, Dachuan ^u   Chen, Ying ^u   Xiao, Yi ^u   London, Nir ^v   Itzhaki, Zohar ^v   Schueler Furman, Ora ^v   Inbar, Yuval ^w   Potapov, Vladimir ^w   Cohen, Mati ^w   Schreiber, Gideon ^w   Tsuchiya, Yuko ^x   Kanamori, Eiji ^y   Standley, Daron M ^z   Nakamura, Haruki ^x   Kinoshita, Kengo ^aa   Driggers, Camden M ^ab   Hall, Robert G ^ab   Morgan, Jessica L ^ab   Hsu, Victor L ^ab   Zhan, Jian ^ac   Yang, Yuedong ^ac   Zhou, Yaoqi ^ac   Kastritis, Panagiotis L ^ad   Bonvin, Alexandre M J J ^ad   Zhang, Weiyi ^ae   Camacho, Carlos J ^ae   Kilambi, Krishna P ^af   Sircar, Aroop ^af   Gray, Jeffrey J ^af   Ohue, Masahito ^ag   Uchikoga, Nobuyuki ^ag   Matsuzaki, Yuri ^ag   Ishida, Takashi ^ag   Akiyama, Yutaka ^ag   Khashan, Raed ^ah   Bush, Stephen ^ah   Fouches, Denis ^ah   Tropsha, Alexander ^ah   Esquivel Rodríguez, Juan ^ai   Kihara, Daisuke ^ai   Stranges, P Benjamin ^aj   Jacak, Ron ^aj   Kuhlman, Brian ^aj   Huang, Sheng You ^ak   Zou, Xiaoqin ^ak   Wodak, Shoshana J ^al,am   Janin, Joel ^an   Baker, David ^a,ao   more..

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b Florida State University   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

^d KITASATO UNIVERSITY   (Japan)

^e IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^f TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^g Seoul National University   (South Korea)

^h UNIVERSITÉ PARIS SACLAY   (France)

ⁱ ÉCOLE POLYTECHNIQUE   (France)

^j LORIA   (France)

^k UMR85 PHYSIOLOGIE DE LA REPRODUCTION ET DES COMPORTEMENTS   (France)

^l CNRS   (France)

^m UNIVERSITÉ DE TOURS   (France)

ⁿ BOGAZICI UNIVERSITY   (Turkey)

^o TEL AVIV UNIVERSITY   (Israel)

^p UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^q BARCELONA SUPERCOMPUTING CENTER   (Spain)

^r INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^s BEIJING UNIVERSITY OF TECHNOLOGY   (China)

^t INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

^u HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^v HEBREW UNIVERSITY   (Israel)

^w WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^x OSAKA UNIVERSITY   (Japan)

^y Koto ku   (Japan)

^z OSAKA UNIVERSITY   (Japan)

^aa TOHOKU UNIVERSITY   (Japan)

^ab OREGON STATE UNIVERSITY   (United States)

^ac Indiana University   (United States)

^ad UTRECHT UNIVERSITY   (Netherlands)

^ae UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^af Johns Hopkins University   (United States)

^ag TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^ah UNIVERSITY OF NORTH CAROLINA   (United States)

^ai Purdue University   (United States)

^aj UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^ak UNIVERSITY OF MISSOURI   (United States)

^al HOSPITAL FOR SICK CHILDREN   (Canada)

^am UNIVERSITY OF TORONTO   (Canada)

^an INSTITUTE FOR INTEGRATIVE BIOLOGY OF THE CELL I2BC   (France)

^ao UNIVERSITY OF WASHINGTON   (United States)

^ap GENENTECH INC   (United States)

more..

Author keywords

computational protein design; conformational plasticity; negative design; protein protein interactions

Indexed keywords

ARTICLE; BINDING SITE; COMPLEX FORMATION; ENERGY TRANSFER; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RIGIDITY;

EID: 80054899738     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.09.031     Document Type: Article

References (20)

1. Fleishman S.J., Whitehead T.A., Ekiert D.C., Dreyfus C., Corn J.E., and Strauch E.M. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin Science 332 2011 816 821
2. Chao G., Lau W.L., Hackel B.J., Sazinsky S.L., Lippow S.M., and Wittrup K.D. Isolating and engineering human antibodies using yeast surface display Nat. Protoc. 1 2006 755 768
3. Janin J., Henrick K., Moult J., Eyck L.T., Sternberg M.J., and Vajda S. CAPRI: a critical assessment of predicted interactions Proteins 52 2003 2 9 (Pubitemid 36648842)
4. Karanicolas J., Corn J.E., Chen I., Joachimiak L.A., Dym O., and Peck S.H. A de novo protein binding pair by computational design and directed evolution Mol. Cell 42 2011 250 260
5. Das R., and Baker D. Macromolecular modeling with rosetta Annu. Rev. Biochem. 77 2008 363 382
6. Ekiert D.C., Bhabha G., Elsliger M.A., Friesen R.H., Jongeneelen M., and Throsby M. Antibody recognition of a highly conserved influenza virus epitope Science 324 2009 246 251
7. Idusogie E.E., Presta L.G., Gazzano-Santoro H., Totpal K., Wong P.Y., and Ultsch M. Mapping of the C1q binding site on rituxan, a chimeric antibody with a human IgG1 Fc J. Immunol. 164 2000 4178 4184 (Pubitemid 30215076)
8. Hwang H., Pierce B., Mintseris J., Janin J., and Weng Z. Protein-protein docking benchmark version 3.0 Proteins 73 2008 705 709 (Pubitemid 352788651)
9. Kastritis P.L., Moal I.H., Hwang H., Weng Z., Bates P.A., Bonvin A.M., and Janin J. A structure-based benchmark for protein-protein binding affinity Protein Sci. 20 2011 482 491
10. Gilson M.K., and Zhou H.X. Calculation of protein-ligand binding affinities Annu. Rev. Biophys. Biomol. Struct. 36 2007 21 42 (Pubitemid 46998108)
11. Sheffler W., and Baker D. RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation Protein Sci. 18 2009 229 239
12. Murali R., Sharkey D.J., Daiss J.L., and Murthy H.M. Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme Proc. Natl Acad. Sci. USA 95 1998 12562 12567 (Pubitemid 28483804)
13. Thompson J.D., Plewniak F., and Poch O. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs Bioinformatics 15 1999 87 88 (Pubitemid 29101202)
14. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., and Cherry J.M. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat. Genet. 25 2000 25 29 (Pubitemid 30257031)
15. Fleishman S.J., Khare S.D., Koga N., and Baker D. Restricted sidechain plasticity in the structures of native proteins and complexes Protein Sci. 20 2011 753 757
16. Grunberg R., Nilges M., and Leckner J. Flexibility and conformational entropy in protein-protein binding Structure 14 2006 683 693
17. Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., and Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations J. Mol. Biol. 331 2003 281 299 (Pubitemid 36870793)
18. Chen R., Li L., and Weng Z. ZDOCK: an initial-stage protein-docking algorithm Proteins 52 2003 80 87 (Pubitemid 36648854)
19. Fleishman S.J., Leaver-Fay A., Corn J.E., Strauch E.M., Khare S.D., and Koga N. RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite PLoS One 6 2011 e20161
20. DeLano W.L. The PyMOL Molecular Graphics System 2002 DeLano Scientific Palo Alto, CA