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Primary Publication

This publication represents a primary interest of the Baker lab

Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection

Scalley-Kim, M., & Baker D. (2004). Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. Journal of molecular biology. 338(3), 573-83.

Primary Publication

Modeling structurally variable regions in homologous proteins with rosetta

Rohl, C. A., Strauss C. E. M., Chivian D., & Baker D. (2004). Modeling structurally variable regions in homologous proteins with rosetta. Proteins. 55(3), 656-77.

Primary Publication

Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation

Qian, B., Ortiz A. R., & Baker D. (2004). Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proceedings of the National Academy of Sciences of the United States of America. 101(43), 15346-51.

Primary Publication

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

Morozov, A. V., Kortemme T., Tsemekhman K., & Baker D. (2004). Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proceedings of the National Academy of Sciences of the United States of America. 101(18), 6946-51.

Primary Publication

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

Misura, K. M. S., Morozov A. V., & Baker D. (2004). Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. Journal of molecular biology. 342(2), 651-64.

Primary Publication

Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins

Kuhn, M., Meiler J., & Baker D. (2004). Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins. 54(2), 282-8.

Primary Publication

Computational design of protein-protein interactions

Kortemme, T., & Baker D. (2004). Computational design of protein-protein interactions. Current opinion in chemical biology. 8(1), 91-7.

Primary Publication

Computational redesign of protein-protein interaction specificity

Kortemme, T., Joachimiak L. A., Bullock A. N., Schuler A. D., Stoddard B. L., & Baker D. (2004). Computational redesign of protein-protein interaction specificity. Nature structural & molecular biology. 11(4), 371-9.

Primary Publication

Protein structure prediction and analysis using the Robetta server

Kim, D. E., Chivian D., & Baker D. (2004). Protein structure prediction and analysis using the Robetta server. Nucleic acids research. 32(Web Server issue), W526-31.

Primary Publication

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

Havranek, J. J., Duarte C. M., & Baker D. (2004). A simple physical model for the prediction and design of protein-DNA interactions. Journal of molecular biology. 344(1), 59-70.

Primary Publication

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