Publications

Preprints are available on bioRxiv.

 

2022

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COLLABORATOR LED

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2021

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COLLABORATOR LED

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2020

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2019

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2018

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2017–1998

ALL PAPERS
437 entries « 14 of 15 »

1999

Engineering and design Journal Article

David Baker, WF DeGrado

In: Current opinion in structural biology, vol. 9, pp. 485-6, 1999, ISSN: 1879-033X.

Chain collapse can occur concomitantly with the rate-limiting step in protein folding Journal Article

K W Plaxco, I S Millett, D J Segel, S Doniach, David Baker

In: Nature structural biology, vol. 6, pp. 554-6, 1999, ISSN: 1072-8368.

Abstract | Links

Matching theory and experiment in protein folding. Journal Article

E Alm, David Baker

In: Current opinion in structural biology, vol. 9, pp. 189-96, 1999, ISSN: 0959-440X.

Abstract

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins Journal Article

K T Simons, I Ruczinski, C Kooperberg, B A Fox, C Bystroff, D Baker

In: Proteins, vol. 34, pp. 82-95, 1999, ISSN: 0887-3585.

Abstract | Links

Ab initio protein structure prediction of CASP III targets using ROSETTA Journal Article

K T Simons, R Bonneau, I Ruczinski, David Baker

In: Proteins, vol. Suppl 3, pp. 171-6, 1999, ISSN: 0887-3585.

Abstract

1998

The single helix in protein L is largely disrupted at the rate-limiting step in folding Journal Article

David E Kim, Q Yi, S T Gladwin, J M Goldberg, David Baker

In: Journal of molecular biology, vol. 284, pp. 807-15, 1998, ISSN: 0022-2836.

Abstract | Links

Metastable states and folding free energy barriers. Journal Article

David Baker

In: Nature structural biology, vol. 5, pp. 1021-4, 1998, ISSN: 1072-8368.

Limited internal friction in the rate-limiting step of a two-state protein folding reaction Journal Article

K W Plaxco, David Baker

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 95, pp. 13591-6, 1998, ISSN: 0027-8424.

Abstract | Links

Clustering of low-energy conformations near the native structures of small proteins Journal Article

D Shortle, K T Simons, David Baker

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 95, pp. 11158-62, 1998, ISSN: 0027-8424.

Abstract | Links

Prediction of local structure in proteins using a library of sequence-structure motifs Journal Article

C Bystroff, D Baker

In: Journal of molecular biology, vol. 281, pp. 565-77, 1998, ISSN: 0022-2836.

Abstract | Links

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain Journal Article

V P Grantcharova, D S Riddle, J V Santiago, David Baker

In: Nature structural biology, vol. 5, pp. 714-20, 1998, ISSN: 1072-8368.

Abstract | Links

The sequences of small proteins are not extensively optimized for rapid folding by natural selection Journal Article

D E Kim, H Gu, D Baker

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 95, pp. 4982-6, 1998, ISSN: 0027-8424.

Abstract | Links

Contributions of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water Journal Article

J A Rank, David Baker

In: Biophysical chemistry, vol. 71, pp. 199-204, 1998, ISSN: 0301-4622.

Abstract

Contact order, transition state placement and the refolding rates of single domain proteins Journal Article

K W Plaxco, K T Simons, David Baker

In: Journal of molecular biology, vol. 277, pp. 985-94, 1998, ISSN: 0022-2836.

Abstract | Links

Simplified proteins: minimalist solutions to the protein folding problem Journal Article

K W Plaxco, D S Riddle, V Grantcharova, David Baker

In: Current opinion in structural biology, vol. 8, pp. 80-5, 1998, ISSN: 0959-440X.

Abstract

Prediction and structural characterization of an independently folding substructure in the src SH3 domain Journal Article

Q Yi, C Bystroff, P Rajagopal, R E Klevit, David Baker

In: Journal of molecular biology, vol. 283, pp. 293-300, 1998, ISSN: 0022-2836.

Abstract | Links

1997

Folding dynamics of the src SH3 domain Journal Article

V P Grantcharova, David Baker

In: Biochemistry, vol. 36, pp. 15685-92, 1997, ISSN: 0006-2960.

Abstract | Links

Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein Journal Article

H Gu, David E Kim, David Baker

In: Journal of molecular biology, vol. 274, pp. 588-96, 1997, ISSN: 0022-2836.

Abstract

Local interactions and the optimization of protein folding Journal Article

R Doyle, K Simons, H Qian, David Baker

In: Proteins, vol. 29, pp. 282-91, 1997, ISSN: 0887-3585.

Abstract | Links

Functional rapidly folding proteins from simplified amino acid sequences Journal Article

D S Riddle, J V Santiago, S T Bray-Hall, N Doshi, V P Grantcharova, Q Yi, David Baker

In: Nature structural biology, vol. 4, pp. 805-9, 1997, ISSN: 1072-8368.

Abstract

Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability Journal Article

M L Scalley, David Baker

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 94, pp. 10636-40, 1997, ISSN: 0027-8424.

Abstract | Links

Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns Journal Article

K F Han, C Bystroff, David Baker

In: Protein science, vol. 6, pp. 1587-90, 1997, ISSN: 0961-8368.

Abstract | Links

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions Journal Article

K T Simons, C Kooperberg, E Huang, David Baker

In: Journal of molecular biology, vol. 268, pp. 209-25, 1997, ISSN: 0022-2836.

Abstract | Links

Kinetics of folding of the IgG binding domain of peptostreptococcal protein L. Journal Article

M L Scalley, Q Yi, H Gu, A McCormack, J R Yates, David Baker

In: Biochemistry, vol. 36, pp. 3373-82, 1997, ISSN: 0006-2960.

Abstract

A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding Journal Article

J A Rank, David Baker

In: Protein science, vol. 6, pp. 347-54, 1997, ISSN: 0961-8368.

Abstract | Links

Blind predictions of local protein structure in CASP2 targets using the I-sites library Journal Article

C Bystroff, David Baker

In: Proteins, vol. Suppl 1, pp. 167-71, 1997, ISSN: 0887-3585.

Abstract | Links

Characterization of the free energy spectrum of peptostreptococcal protein L Journal Article

Q Yi, M L Scalley, K T Simons, S T Gladwin, David Baker

In: Folding & design, vol. 2, pp. 271-80, 1997, ISSN: 1359-0278.

Abstract | Links

1996

Local sequence-structure correlations in proteins Journal Article

C Bystroff, K T Simons, K F Han, David Baker

In: Current opinion in biotechnology, vol. 7, pp. 417-21, 1996, ISSN: 0958-1669.

Abstract | Links

Global properties of the mapping between local amino acid sequence and local structure in proteins Journal Article

K F Han, David Baker

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 93, pp. 5814-8, 1996, ISSN: 0027-8424.

Abstract | Links

Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR Journal Article

Q Yi, David Baker

In: Protein science, vol. 5, pp. 1060-6, 1996, ISSN: 0961-8368.

Abstract | Links

437 entries « 14 of 15 »