1. McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK. (2007). J Mol Biol, Nov 17 [Epub ahead of print].

2. Humphris EL and Kortemme T. Design of multi-specificity in protein interfaces (2007). PLoS Comput Biol. 3(8): 1591-1604.

3. Lengyel CS, Willis LJ, Mann P, Baker D, Kortemme T, Strong RK, McFarland BJ. Mutations designed to destabilize the receptor-bound conformation increases MICA-NKG2D association rate and affinity. J Biol Chem. 2007 Aug 8; [Epub ahead of print].

4. Eames M, Kortemme T. Genome-wide structural mapping of protein interactions reveals differences in abundance- and expression-dependent evolutionary pressures. Structure 15, 1442-1451.

5. Joachimiak LA, Kortemme T, Stoddard BL, Baker D. Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein-Protein Interface. J Mol Biol. Aug 4;361(1):195-208, 2006.

6. Palmer A.E., Giacomello, M., Kortemme, T., Hires, S.A., Lev-Ram, V., Baker, D. & Tsien, R.Y. Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chem Biol. May;13(5):521-30, 2006.

7. Song, G., Lazar G.A., Kortemme, T., Shimaoka, M., Desjarlais, J.R., Baker, D., & Springer, T.A. Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. J Biol Chem. 281, 5042-5049, 2006.

8. Freedman TS, Sondermann H, Friedland GD, Kortemme T, Bar-Sagi D, Marqusee S & Kuriyan J. A Ras-induced conformational switch in the Ras activator Son of sevenless. Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16692-7.

9. Wang SX, Pandey KC, Somoza JR, Sijwali PS, Kortemme T, Brinen LS, Fletterick RJ, Rosenthal PJ & McKerrow JH. Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease. Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11503-8.

10. Morozov, A.V. & Kortemme T. Potential functions for hydrogen bonds in protein structure prediction and design. Adv Protein Chem 2005;72:1-38.

11. Kortemme, T, & Baker, D. A simple physical model for binding energy hotspots in protein protein complexes, Proc Natl Acad Sci U S A 99, 14116-14121, 2002.

12. Chevalier, BS, Kortemme, T, Chadsey, MS, Baker, D, Monnat, RJJr., & Stoddard, BL. Design, activity and structure of E-DreI, a highly site-specific artificial endonuclease. Mol. Cell 10, 895-905, 2002.

13. Gray, JJ, Moughon, S, Kortemme, T, Schueler-Furman, O, Misura, KMS, Morozov, AV, & Baker, D. Protein-protein docking predictions for the CAPRI experiment. Prot. Struct. Funct. Genet. 52, 118-122, 2003.

14. Kortemme, T, Joachimiak, LA, Bullock, AN, Schuler, AD, Stoddard, BL, & Baker, D. Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol 11, 371-379, 2004.

15. Kortemme T, & Baker D. Computational design of protein-protein interactions. Curr Opin Chem Biol 8, 91-97, 2004.

Computational Models & Energy Functions

16. Kortemme, T, Morozov, AV, & Baker, D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein complexes. J. Mol. Biol. 326, 1239-1259, 2003.

17. Morozov, AV, Kortemme, T, & Baker, D. Evaluation of models of electrostatic interactions in proteins. J. Phys. Chem. B 107, 2075-2090, 2003.

18. Kortemme, T, Kim, DE, & Baker, D. Computational alanine scanning of protein-protein interfaces. Sci STKE 2004, pl2, 2004.

19. Morozov, AV, Kortemme, T, Tsemekhman, K, & Baker, D. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci U S A 101, 6946-6951, 2004.

20. Chen Y, Kortemme T, Robertson T, Baker D, & Varani, G. A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res. 32, 147-162, 2004.

21. Jiang, L, Kuhlman, B, Kortemme, T, Baker, D. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 58, 893-904, 2005.

Predictions on Specific Systems

22. McFarland, BJ, Kortemme, T, Baker, D, & Strong, RK. Symmetry recognizing asymmetry: Analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and its MHC class I-like ligand, Structure 11, 411-422, 2003.

23. Boulanger MJ, Bankovich AJ, Kortemme T, Baker D, & Garcia KC. Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130. Mol. Cell 12, 577-589, 2003.

24. Svensson, HG, Wedemeyer, WJ, Ekstrom, JL, Callender, DR, Kortemme, T, Kim, DE, Sjobring, U, & Baker, D. Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain. Biochemistry 43, 2445-2457, 2004.

Peptide Model Systems: Alpha-helices and Beta-sheets

25. Chakrabartty, A, Kortemme, T, Padmanabhan, S, & Baldwin, RL. Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities. Biochemistry 32, 5560-5565, 1993.

26. Chakrabartty, A., Kortemme, T, & Baldwin, RL. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 3, 843-852, 1994.

27. Kortemme, T, Ramirez-Alvarado, M, & Serrano, L. Design of a 20 amino acid three-stranded betasheet protein. Science 281, 253-256, 1998.

28. Ramirez-Alvarado, M, Kortemme, T, Blanco, FJ, & Serrano, L. Beta-hairpin and beta-sheet formation in designed linear peptides. Bioorg Med Chem 7, 93-103, 1999.

29. Lacroix, E, Kortemme, T, Lopez de la Paz, M., & Serrano, L. The design of linear peptides that fold as monomeric beta-sheet structures. Curr Opin Struct Biol 9, 487-93, 1999.

Protein Folding

30. Kortemme, T, Hollecker, M, Kemmink, J, & Creighton, TE. Comparison of the (30-51, 14-38) two-disulphide folding intermediates of the homologous proteins dendrotoxin K and bovine pancreatic trypsin inhibitor by two-dimensional 1H nuclear magnetic resonance. J. Mol. Biol. 257, 188-198, 1996.

31. Kortemme, T, Kelly, MJS, Kay, LE, Forman-Kay, J, & Serrano, L. Similarities between the spectrin SH3 domain denatured state and its folding transition state. J. Mol. Biol. 297, 1217-1229, 2000.

32. Alm, E, Morozov, AV, Kortemme, T, & Baker, D. Simple physical models connect theory and experiment in protein folding kinetics. J. Mol. Biol. 322, 463-476, 2002.

Electrostatic interactions in Thioredoxin-like Proteins

33. Kortemme, T, & Creighton, TE. Ionisation of cysteine residues at the termini of model alpha-helical peptides. Relevance to unusual thiol pKa values in proteins of the thioredoxin family. J. Mol. Biol. 253, 799-812, 1995.

34. Kortemme, T, Darby, NJ, & Creighton, TE. Electrostatic interactions in the active site of the N-terminal thioredoxin-like domain of protein disulfide isomerase. Biochemistry 35, 14503-14511, 1996.

35. Bulaj, G, Kortemme, T, & Goldenberg, DP. Ionization-reactivity relationships for cysteine thiols in polypeptides. Biochemistry 37, 8965-8972, 1998.