Publications

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148 entries « 2 of 8 »
21.

Day, Austin L; Greisen, Per; Doyle, Lindsey; Schena, Alberto; Stella, Nephi; Johnsson, Kai; Baker, David; Stoddard, Barry

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold Journal Article

In: Protein Engineering, Design and Selection, 2018.

Abstract | Links | BibTeX

22.

Park, Hahnbeom; Ovchinnikov, Sergey; Kim, David E.; DiMaio, Frank; Baker, David

Protein homology model refinement by large-scale energy optimization Journal Article

In: Proceedings of the National Academy of Sciences, vol. 115, no. 12, pp. 3054–3059, 2018, ISSN: 0027-8424.

Abstract | Links | BibTeX

23.

Hahnbeom Park Sergey Ovchinnikov, David E. Kim

Protein structure prediction using Rosetta in CASP12 Journal Article

In: Proteins, 2017.

Abstract | Links | BibTeX

24.

Anishchenko, I; Ovchinnikov, S; Kamisetty, H; Baker, D

Origins of coevolution between residues distant in protein 3D structures Journal Article

In: Proceedings of the National Academy of Sciences, vol. 114, no. 34, pp. 9122-9127, 2017.

Abstract | Links | BibTeX

25.

Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A.; Kim, David E.; Kamisetty, Hetunandan; Kyrpides, Nikos C.; Baker, David

Protein structure determination using metagenome sequence data Journal Article

In: Science, vol. 355, no. 6322, pp. 294–298, 2017, ISSN: 0036-8075.

Abstract | Links | BibTeX

26.

Ovchinnikov, Sergey; Park, Hahnbeom; Kim, David E.; Liu, Yuan; Wang, Ray Yu-Ruei; Baker, David

Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11 Journal Article

In: Proteins: Structure, Function, and Bioinformatics, pp. n/a–n/a, 2016, ISSN: 1097-0134.

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27.

Ovchinnikov, S; Kim, DE; Wang, RY; Liu, Y; DiMaio, F; Baker, D

Improved de novo structure prediction in CASP11 by incorporating Co-evolution information into rosetta Journal Article

In: Proteins, 2015.

Abstract | Links | BibTeX

28.

L Kinch S Ovchinnikov, H Park

Large-scale determination of previously unsolved protein structures using evolutionary information Journal Article

In: eLife, 2015.

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29.

Khoury, George A; Liwo, Adam; Khatib, Firas; Zhou, Hongyi; Chopra, Gaurav; Bacardit, Jaume; Bortot, Leandro O; Faccioli, Rodrigo A; Deng, Xin; He, Yi; Krupa, Pawel; Li, Jilong; Mozolewska, Magdalena A; Sieradzan, Adam K; Smadbeck, James; Wirecki, Tomasz; Cooper, Seth; Flatten, Jeff; Xu, Kefan; Baker, David; Cheng, Jianlin; Delbem, Alexandre C B; Floudas, Christodoulos A; Keasar, Chen; Levitt, Michael; Popovi’c, Zoran; Scheraga, Harold A; Skolnick, Jeffrey; Crivelli, Silvia N

WeFold: a coopetition for protein structure prediction. Journal Article

In: Proteins, vol. 82, pp. 1850-68, 2014, ISSN: 1097-0134.

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30.

Chen, Kuang-Yui M; Sun, Jiaming; Salvo, Jason S; Baker, David; Barth, Patrick

High-resolution modeling of transmembrane helical protein structures from distant homologues. Journal Article

In: PLoS computational biology, vol. 10, pp. e1003636, 2014, ISSN: 1553-7358.

Abstract | Links | BibTeX

31.

Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Journal Article

In: eLife, vol. 3, pp. e02030, 2014, ISSN: 2050-084X.

Abstract | Links | BibTeX

32.

Baker, David

Protein folding, structure prediction and design. Journal Article

In: Biochemical Society transactions, vol. 42, pp. 225-9, 2014, ISSN: 1470-8752.

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33.

Moretti, Rocco; Fleishman, Sarel J; Agius, Rudi; Torchala, Mieczyslaw; Bates, Paul A; Kastritis, Panagiotis L; ao P G L M Rodrigues, Jo; Trellet, Mika"el; Bonvin, Alexandre M J J; Cui, Meng; Rooman, Marianne; Gillis, Dimitri; Dehouck, Yves; Moal, Iain; Romero-Durana, Miguel; Perez-Cano, Laura; Pallara, Chiara; Jimenez, Brian; Fernandez-Recio, Juan; Flores, Samuel; Pacella, Michael; Kilambi, Krishna Praneeth; Gray, Jeffrey J; Popov, Petr; Grudinin, Sergei; Esquivel-Rodr’iguez, Juan; Kihara, Daisuke; Zhao, Nan; Korkin, Dmitry; Zhu, Xiaolei; Demerdash, Omar N A; Mitchell, Julie C; Kanamori, Eiji; Tsuchiya, Yuko; Nakamura, Haruki; Lee, Hasup; Park, Hahnbeom; Seok, Chaok; Sarmiento, Jamica; Liang, Shide; Teraguchi, Shusuke; Standley, Daron M; Shimoyama, Hiromitsu; Terashi, Genki; Takeda-Shitaka, Mayuko; Iwadate, Mitsuo; Umeyama, Hideaki; Beglov, Dmitri; Hall, David R; Kozakov, Dima; Vajda, Sandor; Pierce, Brian G; Hwang, Howook; Vreven, Thom; Weng, Zhiping; Huang, Yangyu; Li, Haotian; Yang, Xiufeng; Ji, Xiaofeng; Liu, Shiyong; Xiao, Yi; Zacharias, Martin; Qin, Sanbo; Zhou, Huan-Xiang; Huang, Sheng-You; Zou, Xiaoqin; Velankar, Sameer; Janin, Jo"el; Wodak, Shoshana J; Baker, David

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Journal Article

In: Proteins, vol. 81, pp. 1980-7, 2013, ISSN: 1097-0134.

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34.

Vernon, Robert; Shen, Yang; Baker, David; Lange, Oliver F

Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker. Journal Article

In: Journal of biomolecular NMR, vol. 57, pp. 117-27, 2013, ISSN: 1573-5001.

Abstract | Links | BibTeX

35.

Kamisetty, Hetunandan; Ovchinnikov, Sergey; Baker, David

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 110, pp. 15674-9, 2013, ISSN: 1091-6490.

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36.

van der Schot, Gijs; Zhang, Zaiyong; Vernon, Robert; Shen, Yang; Vranken, Wim F; Baker, David; Bonvin, Alexandre M J J; Lange, Oliver F

Improving 3D structure prediction from chemical shift data. Journal Article

In: Journal of biomolecular NMR, vol. 57, pp. 27-35, 2013, ISSN: 1573-5001.

Abstract | Links | BibTeX

37.

Kim, David E; DiMaio, Frank; Wang, Ray Yu-Ruei; Song, Yifan; Baker, David

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling. Journal Article

In: Proteins, 2013, ISSN: 1097-0134.

Abstract | Links | BibTeX

38.

Kiss, Gert; c"um, Nihan Celebi-"Olc; Moretti, Rocco; Baker, David; Houk, K N

Computational enzyme design Journal Article

In: Angewandte Chemie (International ed. in English), vol. 52, pp. 5700-25, 2013, ISSN: 1521-3773.

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39.

Molski, MA; Goodman, JL; Chou, FC; Baker, D; Das, R; Schepartz, A

Remodeling a beta-peptide bundle Journal Article

In: Chemical Science, vol. 4, pp. 319-324, 2013, ISSN: 2041-6520.

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40.

Krzysiak, Troy C; Jung, Jinwon; Thompson, James; Baker, David; Gronenborn, Angela M

APOBEC2 is a monomer in solution: implications for APOBEC3G models Journal Article

In: Biochemistry, vol. 51, pp. 2008-17, 2012, ISSN: 1520-4995.

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148 entries « 2 of 8 »