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148 entries « 3 of 8 »
41.

Lange, Oliver F; Baker, David

Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation. Journal Article

In: Proteins, vol. 80, pp. 884-95, 2012, ISSN: 1097-0134.

Abstract | Links | BibTeX

42.

Handl, Julia; Knowles, Joshua; Vernon, Robert; Baker, David; Lovell, Simon C

The dual role of fragments in fragment-assembly methods for de novo protein structure prediction Journal Article

In: Proteins, vol. 80, pp. 490-504, 2012, ISSN: 1097-0134.

Abstract | Links | BibTeX

43.

Fleishman, Sarel J; Whitehead, Timothy A; Strauch, Eva-Maria; Corn, Jacob E; Qin, Sanbo; Zhou, Huan-Xiang; Mitchell, Julie C; Demerdash, Omar N A; Takeda-Shitaka, Mayuko; Terashi, Genki; Moal, Iain H; Li, Xiaofan; Bates, Paul A; Zacharias, Martin; Park, Hahnbeom; Ko, Jun-su; Lee, Hasup; Seok, Chaok; Bourquard, Thomas; Bernauer, Julie; Poupon, Anne; Az’e, J’er^ome; Soner, Seren; Ovali, Sefik Kerem; Ozbek, Pemra; Tal, Nir Ben; Haliloglu, T"urkan; Hwang, Howook; Vreven, Thom; Pierce, Brian G; Weng, Zhiping; P’erez-Cano, Laura; Pons, Carles; Fern’andez-Recio, Juan; Jiang, Fan; Yang, Feng; Gong, Xinqi; Cao, Libin; Xu, Xianjin; Liu, Bin; Wang, Panwen; Li, Chunhua; Wang, Cunxin; Robert, Charles H; Guharoy, Mainak; Liu, Shiyong; Huang, Yangyu; Li, Lin; Guo, Dachuan; Chen, Ying; Xiao, Yi; London, Nir; Itzhaki, Zohar; Schueler-Furman, Ora; Inbar, Yuval; Potapov, Vladimir; Cohen, Mati; Schreiber, Gideon; Tsuchiya, Yuko; Kanamori, Eiji; Standley, Daron M; Nakamura, Haruki; Kinoshita, Kengo; Driggers, Camden M; Hall, Robert G; Morgan, Jessica L; Hsu, Victor L; Zhan, Jian; Yang, Yuedong; Zhou, Yaoqi; Kastritis, Panagiotis L; Bonvin, Alexandre M J J; Zhang, Weiyi; Camacho, Carlos J; Kilambi, Krishna P; Sircar, Aroop; Gray, Jeffrey J; Ohue, Masahito; Uchikoga, Nobuyuki; Matsuzaki, Yuri; Ishida, Takashi; Akiyama, Yutaka; Khashan, Raed; Bush, Stephen; Fouches, Denis; Tropsha, Alexander; Esquivel-Rodr’iguez, Juan; Kihara, Daisuke; Stranges, P Benjamin; Jacak, Ron; Kuhlman, Brian; Huang, Sheng-You; Zou, Xiaoqin; Wodak, Shoshana J; Janin, Joel; Baker, David

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

In: Journal of Molecular Biology, vol. 414, pp. 289-302, 2011, ISSN: 1089-8638.

Abstract | Links | BibTeX

44.

Thompson, James; Baker, David

Incorporation of evolutionary information into Rosetta comparative modeling. Journal Article

In: Proteins, vol. 79, pp. 2380-8, 2011, ISSN: 1097-0134.

Abstract | Links | BibTeX

45.

Kellogg, Elizabeth H; Leaver-Fay, Andrew; Baker, David

Role of conformational sampling in computing mutation-induced changes in protein structure and stability Journal Article

In: Proteins, vol. 79, pp. 830-8, 2011, ISSN: 1097-0134.

Abstract | Links | BibTeX

46.

DiMaio, Frank; Leaver-Fay, Andrew; Bradley, Phil; Baker, David; Andr’e, Ingemar

Modeling symmetric macromolecular structures in Rosetta3 Journal Article

In: PloS One, vol. 6, pp. e20450, 2011, ISSN: 1932-6203.

Abstract | Links | BibTeX

47.

Fleishman, Sarel J; Corn, Jacob E; Strauch, Eva M; Whitehead, Tim A; Andre, Ingemar; Thompson, James; Havranek, James J; Das, Rhiju; Bradley, Philip; Baker, David

Rosetta in CAPRI rounds 13-19. Journal Article

In: Proteins, vol. 78, pp. 3212-8, 2010, ISSN: 1097-0134.

Abstract | Links | BibTeX

48.

Tyka, Michael D; Keedy, Daniel A; Andr’e, Ingemar; DiMaio, Frank; Song, Yifan; Richardson, David C; Richardson, Jane S; Baker, David

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping Journal Article

In: Journal of molecular biology, 2010, ISSN: 1089-8638.

Abstract | BibTeX

49.

Cooper, Seth; Khatib, Firas; Treuille, Adrien; Barbero, Janos; Lee, Jeehyung; Beenen, Michael; Leaver-Fay, Andrew; Baker, David; Popovi’c, Zoran; Players, Foldit

Predicting protein structures with a multiplayer online game Journal Article

In: Nature, vol. 466, pp. 756-60, 2010, ISSN: 1476-4687.

Abstract | BibTeX

50.

Blum, Ben; Jordan, Michael I; Baker, David

Feature space resampling for protein conformational search Journal Article

In: Proteins, vol. 78, pp. 1583-93, 2010, ISSN: 1097-0134.

Abstract | BibTeX

51.

Wang, Chu; Vernon, Robert; Lange, Oliver; Tyka, Michael; Baker, David

Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry Journal Article

In: Protein science, vol. 19, pp. 494-506, 2010, ISSN: 1469-896X.

Abstract | BibTeX

52.

Shen, Yang; Bryan, Philip N; He, Yanan; Orban, John; Baker, David; Bax, Ad

De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds Journal Article

In: Protein Science : A Publication of the Protein Society, vol. 19, pp. 349-56, 2010, ISSN: 1469-896X.

Abstract | Links | BibTeX

53.

Raman, Srivatsan; Huang, Yuanpeng J; Mao, Binchen; Rossi, Paolo; Aramini, James M; Liu, Gaohua; Montelione, Gaetano T; Baker, David

Accurate automated protein NMR structure determination using unassigned NOESY data Journal Article

In: Journal of the American Chemical Society, vol. 132, pp. 202-7, 2010, ISSN: 1520-5126.

Abstract | BibTeX

54.

Das, Rhiju; Andr’e, Ingemar; Shen, Yang; Wu, Yibing; Lemak, Alexander; Bansal, Sonal; Arrowsmith, Cheryl H; Szyperski, Thomas; Baker, David

Simultaneous prediction of protein folding and docking at high resolution Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 106, pp. 18978-83, 2009, ISSN: 1091-6490.

Abstract | BibTeX

55.

Kim, David E; Blum, Ben; Bradley, Philip; Baker, David

Sampling bottlenecks in de novo protein structure prediction Journal Article

In: Journal of molecular biology, vol. 393, pp. 249-60, 2009, ISSN: 1089-8638.

Abstract | BibTeX

56.

Davis, Ian W; Raha, Kaushik; Head, Martha S; Baker, David

Blind docking of pharmaceutically relevant compounds using RosettaLigand Journal Article

In: Protein science, vol. 18, pp. 1998-2002, 2009, ISSN: 1469-896X.

Abstract | BibTeX

57.

Kidd, Brian A; Baker, David; Thomas, Wendy E

Computation of conformational coupling in allosteric proteins Journal Article

In: PLoS computational biology, vol. 5, pp. e1000484, 2009, ISSN: 1553-7358.

Abstract | BibTeX

58.

Sadreyev, Ruslan I; Shi, ShuoYong; Baker, David; Grishin, Nick V

Structure similarity measure with penalty for close non-equivalent residues Journal Article

In: Bioinformatics, vol. 25, pp. 1259-63, 2009, ISSN: 1367-4811.

Abstract | BibTeX

59.

Barth, P; Wallner, B; Baker, David

Prediction of membrane protein structures with complex topologies using limited constraints Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 106, pp. 1409-14, 2009, ISSN: 1091-6490.

Abstract | BibTeX

60.

Sheffler, Will; Baker, David

RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation Journal Article

In: Protein science, vol. 18, pp. 229-39, 2009, ISSN: 1469-896X.

Abstract | Links | BibTeX

148 entries « 3 of 8 »