1. Mandell DJ, Kortemme T. (2009). Computer-aided design of functional protein interactions. Nat Chem Biol 5(11):797-807.

2. Mandell DJ, Kortemme T. (2009). Backbone flexibility in computational protein design. Curr Opin Biotechnol 20(4):420-8.

3. Mandell DJ, Coutsias EA, Kortemme T. (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 6:551–552.

4. Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T. (2009). A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol May;5(5):e1000393.

5. Oberdorf R, Kortemme T. (2009). Complex topology rather than complex membership is a determinant of protein dosage sensitivity. Mol Syst Biol. 5:253.

6. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. (2009). Outcome of a workshop on applications of protein models in biomedical research. Structure 17(2):151-9.

7. Babor M and Kortemme T. (2009). Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility. Proteins 75(4):846-58.

8. Freedman TS, Sondermann H, Kuchment O, Friedland GD, Kortemme T, Kuriyan J. (2009). Differences in flexibility underlie functional differences in the ras activators son of sevenless and ras Guanine nucleotide releasing factor 1. Structure 17(1):41-53.

9. Humphris EL, Kortemme T. Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. Structure. (2008). Dec 12;16(12):1777-88.

10. Lauffer BE, Chen S, Melero C, Kortemme T, von Zastrow M, Vargas GA. Engineered protein connectivity to actin mimics PDZ-dependent recycling of GPCRS but not its regulation by HRS. J Biol Chem. (2008). Nov 10.

11. Friedland GD, Linares AJ, Smith CA and Kortemme T. A simple model of backbone flexibility improves modeling of side-chain conformational variability. (2008). J Mol Biol. 380(4):757-74.

12. Smith CA and Kortemme T. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. (2008). J Mol Biol. 380(4):742-56.

13. McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK. A new twist in TCR diversity revealed by a forbidden alphabeta TCR. (2008). J Mol Biol. 375(5):1306-19.

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

15. 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. (2007). J Biol Chem. 282(42):30658-66.

16. Eames M, Kortemme T. Genome-wide structural mapping of protein interactions reveals differences in abundance- and expression-dependent evolutionary pressures. (2007). Structure 15(11):1442-51.

17. 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.

18. 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.

19. 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.

20. 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.

21. 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.

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

23. 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.

24. 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.

25. 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.

26. 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.

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

Computational Models & Energy Functions

28. 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.

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

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

31. 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.

32. 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.

33. 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

34. 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.

35. 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.

36. 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

37. 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.

38. 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.

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

40. 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.

41. 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

42. 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.

43. 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.

44. 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

45. 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.

46. 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.

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