Publications

Preprints are available on bioRxiv.

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142 entries « 1 of 8 »
1.

Dauparas, J.; Anishchenko, I.; Bennett, N.; Bai, H.; Ragotte, R. J.; Milles, L. F.; Wicky, B. I. M.; Courbet, A.; de Haas, R. J.; Bethel, N.; Leung, P. J. Y.; Huddy, T. F.; Pellock, S.; Tischer, D.; Chan, F.; Koepnick, B.; Nguyen, H.; Kang, A.; Sankaran, B.; Bera, A. K.; King, N. P.; Baker, D.

Robust deep learning–based protein sequence design using ProteinMPNN Journal Article

In: Science, 2022.

Abstract | Links | BibTeX

2.

Wang, Jue; Lisanza, Sidney; Juergens, David; Tischer, Doug; Watson, Joseph L.; Castro, Karla M.; Ragotte, Robert; Saragovi, Amijai; Milles, Lukas F.; Baek, Minkyung; Anishchenko, Ivan; Yang, Wei; Hicks, Derrick R.; Expòsit, Marc; Schlichthaerle, Thomas; Chun, Jung-Ho; Dauparas, Justas; Bennett, Nathaniel; Wicky, Basile I. M.; Muenks, Andrew; DiMaio, Frank; Correia, Bruno; Ovchinnikov, Sergey; Baker, David

Scaffolding protein functional sites using deep learning Journal Article

In: Science, 2022.

Abstract | Links | BibTeX

3.

Sen, Neeladri; Anishchenko, Ivan; N, Bordin; Sillitoe, Ian; Velankar, Sameer; Baker, David; Orengo, Christine

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs Journal Article

In: Briefings in Bioinformatics, 2022.

Abstract | Links | BibTeX

4.

Linder, Johannes; La Fleur, Alyssa; Chen, Zibo; Ljubetič, Ajasja; Baker, David; Kannan, Sreeram; Seelig, Georg

Interpreting neural networks for biological sequences by learning stochastic masks Journal Article

In: Nature Machine Intelligence, 2022.

Abstract | Links | BibTeX

5.

Baek, Minkyung; Baker, David

Deep learning and protein structure modeling Journal Article

In: Nature Methods, 2022.

Abstract | Links | BibTeX

6.

Du, Zongyang; Su, Hong; Wang, Wenkai; Ye, Lisha; Wei, Hong; Peng, Zhenling; Anishchenko, Ivan; Baker, David; Yang, Jianyi

The trRosetta server for fast and accurate protein structure prediction Journal Article

In: Nature Protocols, 2021.

Abstract | Links | BibTeX

7.

Anishchenko, Ivan; Pellock, Samuel J.; Chidyausiku, Tamuka M.; Ramelot, Theresa A.; Ovchinnikov, Sergey; Hao, Jingzhou; Bafna, Khushboo; Norn, Christoffer; Kang, Alex; Bera, Asim K.; DiMaio, Frank; Carter, Lauren; Chow, Cameron M.; Montelione, Gaetano T.; Baker, David

De novo protein design by deep network hallucination Journal Article

In: Nature, 2021.

Abstract | Links | BibTeX

8.

Baek, Minkyung; Anishchenko, Ivan; Park, Hahnbeom; Humphreys, Ian R.; Baker, David

Protein oligomer modeling guided by predicted inter-chain contacts in CASP14 Journal Article

In: Proteins, 2021.

Abstract | Links | BibTeX

9.

Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan; Dauparas, Justas; Ovchinnikov, Sergey; Lee, Gyu Rie; Wang, Jue; Cong, Qian; Kinch, Lisa N.; Schaeffer, R. Dustin; Millán, Claudia; Park, Hahnbeom; Adams, Carson; Glassman, Caleb R.; DeGiovanni, Andy; Pereira, Jose H.; Rodrigues, Andria V.; van Dijk, Alberdina A.; Ebrecht, Ana C.; Opperman, Diederik J.; Sagmeister, Theo; Buhlheller, Christoph; Pavkov-Keller, Tea; Rathinaswamy, Manoj K.; Dalwadi, Udit; Yip, Calvin K.; Burke, John E.; Garcia, K. Christopher; Grishin, Nick V.; Adams, Paul D.; Read, Randy J.; Baker, David

Accurate prediction of protein structures and interactions using a three-track neural network Journal Article

In: Science, 2021.

Abstract | Links | BibTeX

10.

Norn, Christoffer; Wicky, Basile I. M.; Juergens, David; Liu, Sirui; Kim, David; Tischer, Doug; Koepnick, Brian; Anishchenko, Ivan; Baker, David; Ovchinnikov, Sergey

Protein sequence design by conformational landscape optimization Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 11, 2021.

Abstract | Links | BibTeX

11.

Hiranuma, Naozumi; Park, Hahnbeom; Baek, Minkyung; Anishchenko, Ivan; Dauparas, Justas; Baker, David

Improved protein structure refinement guided by deep learning based accuracy estimation Journal Article

In: Nature Communications, vol. 12, no. 1340, 2021.

Abstract | Links | BibTeX

12.

Park, Hahnbeom; Zhou, Guangfeng; Baek, Minkyung; Baker, David; DiMaio, Frank

Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking Journal Article

In: Journal of Chemical Theory and Computation, 2021.

Abstract | Links | BibTeX

13.

Yang, Jianyi; Anishchenko, Ivan; Park, Hahnbeom; Peng, Zhenling; Ovchinnikov, Sergey; Baker, David

Improved protein structure prediction using predicted interresidue orientations Journal Article

In: Proceedings of the National Academy of Sciences, 2020, ISBN: 0027-8424.

Abstract | Links | BibTeX

14.

Wu, Qi; Peng, Zhenling; Anishchenko, Ivan; Cong, Qian; Baker, David; Yang, Jianyi

Protein contact prediction using metagenome sequence data and residual neural networks Journal Article

In: Bioinformatics, vol. 36, no. 1, 2019.

Abstract | Links | BibTeX

15.

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

16.

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

17.

Hahnbeom Park Sergey Ovchinnikov, David E. Kim

Protein structure prediction using Rosetta in CASP12 Journal Article

In: Proteins, 2017.

Abstract | Links | BibTeX

18.

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

19.

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

20.

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.

Abstract | Links | BibTeX

142 entries « 1 of 8 »

 

2022

FROM THE LAB

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Dauparas, J. and Anishchenko, I. and Bennett, N. and Bai, H. and Ragotte, R. J. and Milles, L. F. and Wicky, B. I. M. and Courbet, A. and de Haas, R. J. and Bethel, N. and Leung, P. J. Y. and Huddy, T. F. and Pellock, S. and Tischer, D. and Chan, F. and Koepnick, B. and Nguyen, H. and Kang, A. and Sankaran, B. and Bera, A. K. and King, N. P. and Baker, D.

Robust deep learning–based protein sequence design using ProteinMPNN Journal Article

In: Science, 2022.

Abstract | Links

Jue Wang, Sidney Lisanza, David Juergens, Doug Tischer, Joseph L. Watson, Karla M. Castro, Robert Ragotte, Amijai Saragovi, Lukas F. Milles, Minkyung Baek, Ivan Anishchenko, Wei Yang, Derrick R. Hicks, Marc Expòsit, Thomas Schlichthaerle, Jung-Ho Chun, Justas Dauparas, Nathaniel Bennett, Basile I. M. Wicky, Andrew Muenks, Frank DiMaio, Bruno Correia, Sergey Ovchinnikov, David Baker

Scaffolding protein functional sites using deep learning Journal Article

In: Science, 2022.

Abstract | Links

Minkyung Baek, David Baker

Deep learning and protein structure modeling Journal Article

In: Nature Methods, 2022.

Abstract | Links

COLLABORATOR LED

Show all

Sen, Neeladri and Anishchenko, Ivan and Bordin N and Sillitoe, Ian and Velankar, Sameer and Baker, David and Orengo, Christine

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs Journal Article

In: Briefings in Bioinformatics, 2022.

Abstract | Links

Linder, Johannes, La Fleur, Alyssa, Chen, Zibo, Ljubetič, Ajasja, Baker, David, Kannan, Sreeram, Seelig, Georg

Interpreting neural networks for biological sequences by learning stochastic masks Journal Article

In: Nature Machine Intelligence, 2022.

Abstract | Links

2021

FROM THE LAB

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Anishchenko, Ivan and Pellock, Samuel J. and Chidyausiku, Tamuka M. and Ramelot, Theresa A. and Ovchinnikov, Sergey and Hao, Jingzhou and Bafna, Khushboo and Norn, Christoffer and Kang, Alex and Bera, Asim K. and DiMaio, Frank and Carter, Lauren and Chow, Cameron M. and Montelione, Gaetano T. and Baker, David

De novo protein design by deep network hallucination Journal Article

In: Nature, 2021.

Abstract | Links

Minkyung Baek, Ivan Anishchenko, Hahnbeom Park, Ian R. Humphreys, David Baker

Protein oligomer modeling guided by predicted inter-chain contacts in CASP14 Journal Article

In: Proteins, 2021.

Abstract | Links

Baek, Minkyung and DiMaio, Frank and Anishchenko, Ivan and Dauparas, Justas and Ovchinnikov, Sergey and Lee, Gyu Rie and Wang, Jue and Cong, Qian and Kinch, Lisa N. and Schaeffer, R. Dustin and Millán, Claudia and Park, Hahnbeom and Adams, Carson and Glassman, Caleb R. and DeGiovanni, Andy and Pereira, Jose H. and Rodrigues, Andria V. and van Dijk, Alberdina A. and Ebrecht, Ana C. and Opperman, Diederik J. and Sagmeister, Theo and Buhlheller, Christoph and Pavkov-Keller, Tea and Rathinaswamy, Manoj K. and Dalwadi, Udit and Yip, Calvin K. and Burke, John E. and Garcia, K. Christopher and Grishin, Nick V. and Adams, Paul D. and Read, Randy J. and Baker, David

Accurate prediction of protein structures and interactions using a three-track neural network Journal Article

In: Science, 2021.

Abstract | Links

Norn, Christoffer, Wicky, Basile I. M., Juergens, David, Liu, Sirui, Kim, David, Tischer, Doug, Koepnick, Brian, Anishchenko, Ivan, Baker, David, Ovchinnikov, Sergey

Protein sequence design by conformational landscape optimization Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 11, 2021.

Abstract | Links

COLLABORATOR LED

Show all

Du, Zongyang and Su, Hong and Wang, Wenkai and Ye, Lisha and Wei, Hong and Peng, Zhenling and Anishchenko, Ivan and Baker, David and Yang, Jianyi

The trRosetta server for fast and accurate protein structure prediction Journal Article

In: Nature Protocols, 2021.

Abstract | Links

Naozumi Hiranuma, Hahnbeom Park, Minkyung Baek, Ivan Anishchenko, Justas Dauparas, David Baker

Improved protein structure refinement guided by deep learning based accuracy estimation Journal Article

In: Nature Communications, vol. 12, no. 1340, 2021.

Abstract | Links

Hahnbeom Park, Guangfeng Zhou, Minkyung Baek, David Baker, Frank DiMaio

Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking Journal Article

In: Journal of Chemical Theory and Computation, 2021.

Abstract | Links

2020

FROM THE LAB

Show all

Yang, Jianyi, Anishchenko, Ivan, Park, Hahnbeom, Peng, Zhenling, Ovchinnikov, Sergey, Baker, David

Improved protein structure prediction using predicted interresidue orientations Journal Article

In: Proceedings of the National Academy of Sciences, 2020, ISBN: 0027-8424.

Abstract | Links

COLLABORATOR LED

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Sorry, no publications matched your criteria.

2019

FROM THE LAB

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Sorry, no publications matched your criteria.

COLLABORATOR LED

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Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang

Protein contact prediction using metagenome sequence data and residual neural networks Journal Article

In: Bioinformatics, vol. 36, no. 1, 2019.

Abstract | Links

2018

FROM THE LAB

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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

COLLABORATOR LED

Show all

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

2017–1998

ALL PAPERS

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126 entries « 1 of 5 »

2017

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

Protein structure prediction using Rosetta in CASP12 Journal Article

In: Proteins, 2017.

Abstract | Links

I Anishchenko, S Ovchinnikov, H Kamisetty, D Baker

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

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

Protein structure determination using metagenome sequence data Journal Article

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

Abstract | Links

2016

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.

Abstract | Links

2015

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

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

In: Proteins, 2015.

Abstract | Links

S Ovchinnikov, L Kinch, H Park, Y Liao, J Pei, DE Kim, H Kamisetty, NV Grishin, D Baker

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

In: eLife, 2015.

Abstract | Links

2014

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

WeFold: a coopetition for protein structure prediction. Journal Article

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

Abstract | Links

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

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

Sergey Ovchinnikov, Hetunandan Kamisetty, David Baker

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

David Baker

Protein folding, structure prediction and design. Journal Article

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

Abstract | Links

2013

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

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.

Abstract | Links

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

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

Hetunandan Kamisetty, Sergey Ovchinnikov, David Baker

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.

Abstract | Links

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

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

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

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

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

Computational enzyme design Journal Article

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

Abstract | Links

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

Remodeling a beta-peptide bundle Journal Article

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

Abstract | Links

2012

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

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

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

Abstract | Links

Oliver F Lange, David Baker

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

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

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

2011

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

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

James Thompson, David Baker

Incorporation of evolutionary information into Rosetta comparative modeling. Journal Article

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

Abstract | Links

Elizabeth H Kellogg, Andrew Leaver-Fay, David Baker

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

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

Modeling symmetric macromolecular structures in Rosetta3 Journal Article

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

Abstract | Links

2010

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

Rosetta in CAPRI rounds 13-19. Journal Article

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

Abstract | Links

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

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

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

Abstract

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

Predicting protein structures with a multiplayer online game Journal Article

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

Abstract

Ben Blum, Michael I Jordan, David Baker

Feature space resampling for protein conformational search Journal Article

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

Abstract

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

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

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

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

126 entries « 1 of 5 »