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Primary Publication

This publication represents a primary interest of the Baker lab

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

Simons, K. T., Ruczinski I., Kooperberg C., Fox B. A., Bystroff C., & Baker D. (1999). Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins. 34(1), 82-95.

Primary Publication

Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics

Plaxco, K. W., Simons K. T., Ruczinski I., & Baker D. (2000). Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry. 39(37), 11177-83.

Primary Publication

Ageneral expressionforbimolecularassociationrates withorientational constraints

Schlosshauer, M., & Baker D. (2002). Ageneral expressionforbimolecularassociationrates withorientational constraints. Physical Chemistry B.

Primary Publication

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Accurate computer-based design of a new backbone conformation in the second turn of protein L

Kuhlman, B., O'Neill J. W., Kim D. E., Zhang K. Y. J., & Baker D. (2002). Accurate computer-based design of a new backbone conformation in the second turn of protein L. Journal of molecular biology. 315(3), 471-7.

Primary Publication

Assigning function to yeast proteins by integration of technologies

Hazbun, T. R., Malmström L., Anderson S., Graczyk B. J., Fox B., Riffle M., et al. (2003). Assigning function to yeast proteins by integration of technologies. Molecular cell. 12(6), 1353-65.

Primary Publication

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

Kim, D. E., Gu H., & Baker D. (1998). The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proceedings of the National Academy of Sciences of the United States of America. 95(9), 4982-6.

Primary Publication

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

Bystroff, C., & Baker D. (1998). Prediction of local structure in proteins using a library of sequence-structure motifs. Journal of molecular biology. 281(3), 565-77.

Primary Publication

Comparison of Quantum Mechanics and Molecular Mechanics Dimerization Energy Landscapes for Pairs of Ring-Containing Amino Acids in Proteins

AV, M., KMS M., K T., & D B. (2004). Comparison of Quantum Mechanics and Molecular Mechanics Dimerization Energy Landscapes for Pairs of Ring-Containing Amino Acids in Proteins. Journal of Physical Chemistry B .

Primary Publication

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Computational alanine scanning of protein-protein interfaces

Kortemme, T., Kim D. E., & Baker D. (2004). Computational alanine scanning of protein-protein interfaces. Science's STKE. 2004(219), pl2.

Primary Publication

Structure prediction for CASP8 with all-atom refinement using Rosetta

Raman, S., Vernon R., Thompson J., Tyka M., Sadreyev R., Pei J., et al. (2009). Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77 Suppl 9, 89-99.

Primary Publication

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