Publications

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148 entries « 5 of 8 »
81.

Baker, David

Prediction and design of macromolecular structures and interactions Journal Article

In: Philosophical transactions of the Royal Society of London, vol. 361, pp. 459-63, 2006, ISSN: 0962-8436.

Abstract | Links | BibTeX

82.

Thompson, Michael J; Sievers, Stuart A; Karanicolas, John; Ivanova, Magdalena I; Baker, David; Eisenberg, David

The 3D profile method for identifying fibril-forming segments of proteins Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 103, pp. 4074-8, 2006, ISSN: 0027-8424.

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83.

Yarov-Yarovoy, Vladimir; Schonbrun, Jack; Baker, David

Multipass membrane protein structure prediction using Rosetta Journal Article

In: Proteins, vol. 62, pp. 1010-25, 2006, ISSN: 1097-0134.

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84.

Arakaki, Tracy; Trong, Isolde Le; Phizicky, Eric; Quartley, Erin; Detitta, George; Luft, Joseph; Lauricella, Angela; Anderson, Lori; Kalyuzhniy, Oleksandr; Worthey, Elizabeth; Myler, Peter J; Kim, David; Baker, David; Hol, Wim G J; Merritt, Ethan A

Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major Journal Article

In: Acta crystallographica. Section F, Structural biology and crystallization communications, vol. 62, pp. 175-9, 2006, ISSN: 1744-3091.

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85.

Schueler-Furman, Ora; Wang, Chu; Bradley, Phil; Misura, Kira; Baker, David

Progress in modeling of protein structures and interactions Journal Article

In: Science, vol. 310, pp. 638-42, 2005, ISSN: 1095-9203.

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86.

Bradley, Philip; Misura, Kira M S; Baker, David

Toward high-resolution de novo structure prediction for small proteins Journal Article

In: Science, vol. 309, pp. 1868-71, 2005, ISSN: 1095-9203.

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87.

Schueler-Furman, Ora; Wang, Chu; Baker, David

Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility Journal Article

In: Proteins, vol. 60, pp. 187-94, 2005, ISSN: 1097-0134.

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88.

Wang, Chu; Schueler-Furman, Ora; Baker, David

Improved side-chain modeling for protein-protein docking Journal Article

In: Protein science, vol. 14, pp. 1328-39, 2005, ISSN: 0961-8368.

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89.

Misura, Kira M S; Baker, David

Progress and challenges in high-resolution refinement of protein structure models Journal Article

In: Proteins, vol. 59, pp. 15-29, 2005, ISSN: 1097-0134.

Abstract | Links | BibTeX

90.

Meiler, Jens; Baker, David

The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy Journal Article

In: Journal of magnetic resonance, vol. 173, pp. 310-6, 2005, ISSN: 1090-7807.

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91.

Jiang, Lin; Kuhlman, Brian; Kortemme, Tanja; Baker, David

A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces Journal Article

In: Proteins, vol. 58, pp. 893-904, 2005, ISSN: 1097-0134.

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92.

Saunders, Christopher T; Baker, David

Recapitulation of protein family divergence using flexible backbone protein design Journal Article

In: Journal of molecular biology, vol. 346, pp. 631-44, 2005, ISSN: 0022-2836.

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93.

Kim, David E; Chivian, Dylan; Malmstr"om, Lars; Baker, David

Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM Journal Article

In: Proteins, vol. 61 Suppl 7, pp. 193-200, 2005, ISSN: 1097-0134.

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94.

na, Osvaldo Gra; Baker, David; MacCallum, Robert M; Meiler, Jens; Punta, Marco; Rost, Burkhard; Tress, Michael L; Valencia, Alfonso

CASP6 assessment of contact prediction Journal Article

In: Proteins, vol. 61 Suppl 7, pp. 214-24, 2005, ISSN: 1097-0134.

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95.

Bradley, Philip; Malmstr"om, Lars; Qian, Bin; Schonbrun, Jack; Chivian, Dylan; Kim, David E; Meiler, Jens; Misura, Kira M S; Baker, David

Free modeling with Rosetta in CASP6 Journal Article

In: Proteins, vol. 61 Suppl 7, pp. 128-34, 2005, ISSN: 1097-0134.

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96.

Cheng, Gong; Qian, Bin; Samudrala, Ram; Baker, David

Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design Journal Article

In: Nucleic acids research, vol. 33, pp. 5861-7, 2005, ISSN: 1362-4962.

Abstract | Links | BibTeX

97.

Chivian, Dylan; Kim, David E; Malmstr"om, Lars; Schonbrun, Jack; Rohl, Carol A; Baker, David

Prediction of CASP6 structures using automated Robetta protocols Journal Article

In: Proteins, vol. 61 Suppl 7, pp. 157-66, 2005, ISSN: 1097-0134.

Abstract | Links | BibTeX

98.

Morozov, Alexandre V; Havranek, James J; Baker, David; Siggia, Eric D

Protein-DNA binding specificity predictions with structural models Journal Article

In: Nucleic acids research, vol. 33, pp. 5781-98, 2005, ISSN: 1362-4962.

Abstract | BibTeX

99.

Havranek, James J; Duarte, Carlos M; Baker, David

A simple physical model for the prediction and design of protein-DNA interactions Journal Article

In: Journal of molecular biology, vol. 344, pp. 59-70, 2004, ISSN: 0022-2836.

Abstract | Links | BibTeX

100.

Misura, Kira M S; Morozov, Alexandre V; Baker, David

Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction Journal Article

In: Journal of molecular biology, vol. 342, pp. 651-64, 2004, ISSN: 0022-2836.

Abstract | Links | BibTeX

148 entries « 5 of 8 »