The Art of Molecular Driving Forces
1. Dill, K. A. and M. Troll. FET Programs Op Amp for Invertible Gain. Electronics 113, Jan. 9 (1975).
2. Dill, K. A. and R.H. Shafer. Radial Migration of DNA Molecules in Cylindrical Flow. III. Circles and the Effect of Non-Gaussian Polymer Statistics. Biophysical Chemistry 4: 51 (1976).
3. Dill, K.A. Theory for the Separation of Very Large DNA Molecules by Radial Migration. Biophysical Chemistry 10: 327 (1979).
4. Dill, K.A., and B.H. Zimm. A Rheological Separator for Very Large DNA Molecules. Nucleic Acids Research 7: 735 (1979).
5. Dill, K.A. Chain Folding in Semicrystalline Polymers. Faraday Discussion, Chemical Society 68: 104, 452 (1979).
6. Dill, K.A. and B.H. Zimm. Stress- and Strain-Relaxation Dynamics of Polymer Solutions: I. Theory for an Instrument. Macromolecules 13: 426 (1980).
7. Dill, K.A. and B.H. Zimm. Dynamics of Polymer Solutions I. Theory for an Instrument. Macromolecules 13: 426 (1980).
8. Dill, K.A. and B.H. Zimm. Dynamics of Polymer Solutions: II. The Determination of Molecular Weight Distribution by Viscoelasticity. Macromolecules 13: 432 (1980).
9. Troll, M., K.A. Dill, and B.H. Zimm. Dynamics of Polymer Solutions: III. An Instrument for Stress Relaxations on Dilute Solutions of Large Polymer Molecules. Macromolecules 13: 436 (1980).
10. Dill, K.A. Dynamics of Polymer Solutions: IV. Shear-Stress Relaxation Experiments on Solutions of DNA from Bacteriophage T2. Macromolecules 13: 438 (1980).
11. Dill, K.A. Concentration Dependence of the Viscosity and Viscoelasticity of Polymer Solutions: Application of the Theory of Muthukumar and Freed. Macromolecules 13: 620 (1980).
12. Dill, K.A. and P.J. Flory. Interphases of Chain Molecules: Monolayers and Lipid Bilayer Membranes. Proceedings of the National Academy of Sciences USA 77: 3115 (1980).
13. Dill, K.A. and P.J. Flory. Molecular Organization in Micelles and Vesicles. Proceedings of the National Academy of Sciences USA 78: 676 (1981).
14. Tullis, R.H., K.A. Dill, and P.A. Price. Fluorescence and Kinetic Studies on the Divalent Metal Ion Induced Conformational Changes in DNaseA. Journal of Biological Chemistry 256: 5656 (1981).
15. Dill, K.A. Configurations of Amphiphilic Molecules in Micelles. Journal of Physical Chemistry 86: 1498 (1982).
16. Dill, K.A. Molecular Organization in Amphiphilic Aggregates. In Surfactants in Solution. K.L. Mittal, ed. New York: Plenum Press, 1983.
17. Flory, P.J., D.Y. Yoon, and K.A. Dill. The Interphase in Lamellar Semicrystalline Polymers. Macromolecules 17: 862-868 (1984).
18. Dill, K.A. and R.S. Cantor. Statistical Thermodynamics of Short Chain Molecule Interphases I. Theory. Macromolecules 17: 380-384 (1984).
19. Cantor, R.S. and K.A. Dill. Statistical Thermodynamics of Short Chain Molecule Interphases II. Configurational Properties of Amphiphilic Aggregates. Macromolecules 17: 384-388 (1984).
20. Dill, K.A., D.E. Koppel, R.S. Cantor, J.D. Dill, D. Bendedouch, and S.H. Chen. The Molecular Conformations in Surfactant Micelles. Nature 309: 42-45 (1984).
21. Marqusee, J.A., M. Warner, and K.A. Dill. Frequency Dependence of NMR Relaxation Rates in Bilayer Membranes. Journal of Chemical Physics 81: 6404 (1984).
22. Chen, S.H. and K.A. Dill. Comment: Water in the Hydrocarbon Core of Micelles. Nature 314: 385 (1985).
23. Dill, K.A. Theory for the Folding and Stability of Globular Proteins. Biochemistry 24: 1501 (1985).
24. Dill, K.A. Comment: Molecular Conformations in Surfactant Micelles. Nature 313: 603 (1985).
25. Cantor, R.S. and K.A. Dill. Statistical Thermodynamic Theory for the Melting of n-Alkanes from Their Rotator Phases. Macromolecules 18: 1875 (1985).
26. Dill, K.A. and R.S. Cantor. The Statistical Thermodynamics of Surfactant Aggregates. In Physics of Amphiphiles: Micelles, Vesicles, and Microemulsions, p. 376. V. Degiorgio, and M. Corti, eds. Amsterdam: North Holland, 1986.
27. Dill, K.A. The Chain Conformations in Membranes and Micelles. Advances in Colloid and Interface Science 26: 99 (1986).
28. Cantor, R.S. and K.A. Dill. Theory for the Equation of State of Phospholipid Monolayers. Langmuir 2: 331 (1986).
29. Marqusee, J.A. and K.A. Dill. Solute Partitioning into Chain Molecule Interphases: Monolayers, Bilayer Membranes and Micelles. Journal of Chemical Physics 85: 434 (1986).
30. Marqusee, J.A. and K.A. Dill. Chain Configurations in Lamellar Semicrystalline Polymer Interphases. Macromolecules 19: 2420 (1986).
31. Stigter, D. and K.A. Dill. Interactions in Dilute Monolayers of Long Chain Ions at the Interface Between n-Heptane and Aqueous Salt Solutions. Langmuir 2: 791 (1986).
32. Dill, K.A. The Stabilities of Globular Proteins. In Protein Engineering, p. 187. D.L. Oxender and C.F. Fox, eds. Alan R. Liss, Inc., 1987.
33. Dill, K.A. The Mechanism of Solute Retention in Reversed Phase Liquid Chromatography Journal of Physical Chemistry 91: 1980 (1987).
34. Dill, K.A. Protein Surgery. Protein Engineering 1: 369-372 (1987).
35. Stigter, D. and K.A. Dill. Lateral Interactions Among Phospholipid Headgroups at the Heptane/Water Interface. Langmuir 4: 200-209 (1988).
36. Dill, K.A. and D. Stigter. Lateral Interactions Among PC and PE Headgroups in Phospholipid Monolayers and Bilayers. Biochemistry 27: 3446-3453 (1988).
37. DeYoung, L. and K.A. Dill. Solute Partitioning into Lipid Bilayer Membranes. Biochemistry 27: 5281-5289 (1988).
38. Dill, K.A., J. Naghizadeh, and J. A. Marqusee. Chain Molecules at High Densities at Interfaces. Annual Review of Physical Chemistry 39: 425-461 (1988).
39. Dill, K.A. and D.O.V. Alonso. Conformational Entropy and Protein Stability. In Protein Structure and Protein Engineering, 39, pp. 51-58. R. Huber, and E.L. Winnacker, eds. Colloquium-Mosbach der Gesellschaft fur Biologische Chemie. Berlin: Springer-Verlag, 1988.
40. Ying, P.T., J.G. Dorsey, and K.A. Dill. Retention Mechanisms of Reversed Phase Liquid Chromatography: Determination of Solute-Solvent Interaction Free Energies. Analytical Chemistry 61: 2540-2546 (1989).
41. Chan, H.S. and K.A. Dill. Intra-Chain Loops in Polymers: Effects of Excluded Volume. Journal of Chemical Physics 90: 492-509 (1989).
42. Dill, K.A., D.O.V. Alonso, and K. Hutchinson. Thermal Stabilities of Globular Proteins. Biochemistry 28: 5439-5449 (1989).
43. Dorsey, J.G. and K.A. Dill. The Molecular Mechanism of Retention in Reversed-Phase Liquid Chromatography. Chemical Reviews 89: 331-346 (1989).
44. Lau, K.F. and K.A. Dill. A Lattice Statistical Mechanics Model of the Conformational and Sequence Spaces of Proteins. Macromolecules 22: 3986-3997 (1989).
45. Stigter, D. and K.A. Dill. Free Energy of Electrical Double Layers: Entropy of Adsorbed Ions and the Binding Polynomial. Journal of Physical Chemistry 93: 6737-6743 (1989).
46. Chan, H.S. and K.A. Dill. Compact Polymers. Macromolecules 22: 4559-4573 (1989).
47. DeYoung, L.R. and K.A. Dill. Partitioning of Nonpolar Solutes into Bilayers and Amorphous n-Alkanes. Journal of Physical Chemistry 94: 801-809 (1990).
48. Stigter, D. and K.A. Dill. Charge Effects on Folded and Unfolded Proteins. Biochemistry 29: 1262-1271 (1990).
49. Lau, K.F. and K.A. Dill. Theory for Protein Mutability and Biogenesis. Proceedings of the National Academy of Sciences USA 87: 638-642 (1990).
50. Chan, H.S. and K.A. Dill. The Effects of Internal Constraints on the Configurations of Chain Molecules. Journal of Chemical Physics 92: 3118-3135 (1990).
51. Dill, K.A. Review of Lipid and Biopolymer Monolayers at Liquid Interfaces. Journal of the American Chemical Society 112: 1299 (1990).
52. Dill, K.A. Dominant Forces in Protein Folding. Biochemistry 29: 7133-7155 (1990). (PDF)
53. Chan, H.S. and K.A. Dill. Origins of Structure in Globular Proteins. Proceedings of the National Academy of Sciences USA 87: 6388 (1990).
54. Dill, K.A. The Meaning of Hydrophobicity. Science 250: 297-298 (1990).
55. Wattenbarger, M.R., H.S. Chan, D.F. Evans, V.A. Bloomfield, and K.A. Dill. Surface-Induced Enhancement of Internal Structure in Polymers and Proteins. Journal of Chemical Physics 93: 8343 (1990).
56. Chan. H.S. and K.A. Dill. Polymer Principles in Protein Structure and Stability. Annual Review of Biophysics and Biophysical Chemistry 20: 447-490 (1991).
57. Dill, K.A. and D. Shortle. Denatured States of Proteins. Annual Review of Biochemistry 60: 795-825 (1991).
58. Chan, H.S. and K.A. Dill. "Sequence Space Soup" of Proteins and Copolymers. Journal of Chemical Physics 95: 3775-3787 (1991).
59. Stigter, D., D.O.V. Alonso, and K.A. Dill. Protein Stability: Electrostatics and Compact Denatured States Proceedings of the National Academy of Sciences USA 88: 4176-4180 (1991).
60. Alonso, D.O.V. and K.A. Dill. Solvent Denaturation and Stabilization of Globular Proteins. Biochemistry 30: 5974-5985 (1991). (PDF)
61. Naghizadeh, J. and K.A. Dill. Statistical Mechanics of Chain Molecules at Interfaces Macromolecules 24: 1768-1778 (1991).
62. Chan, H.S., M.R. Wattenbarger, D.F. Evans, V.A. Bloomfield, and K.A. Dill. Enhanced Structure in Polymers at Interfaces. Journal of Chemical Physics 94: 8542-8557 (1991).
63. Kollman, P.A. and K.A. Dill. Decisions in Force Field Development: An Alternative to Those Described by Roterman et al. Journal of Biomolecular Structure & Dynamics 8: 1103-1107 (1991).
64. Alonso, D.O.V., K.A. Dill, and D. Stigter. The Three States of Globular Proteins: Acid Denaturation. Biopolymers 31: 1631-1649 (1991).
65. Miller, R., C.A. Danko, M.J. Fasolka, A.C. Balazs, H.S. Chan, and K.A. Dill. Folding kinetics of proteins and copolymers. Journal of Chemical Physics 96: 768-780 (1992).
66. Shortle, D., H.S. Chan, and K.A. Dill. Modeling the Effects of Mutations on the Denatured States of Proteins. Protein Science 1: 201-215 (1992).
67. Yue, K. and K.A. Dill. Inverse Protein Folding Problem: Designing Polymer Sequences. Proceedings of the National Academy of Sciences USA 89: 4163-4167 (1992).
68. Cole, L.A., J.G. Dorsey, and K.A. Dill. Temperature Dependence of Retention in Reversed-Phase Liquid Chromatography: II. Mobile Phase Considerations. Analytical Chemistry 64: 1324-1327 (1992).
69. Mingins, J., D. Stigter, and K.A. Dill. Phospholipid Interactions in Model Membrane Systems. I. Experiments on Monolayers. Biophysical Journal 61: 1603-1615 (1992).
70. Stigter, D., J. Mingins, and K.A. Dill. Phospholipid Interactions in Model Membrane Systems. II. Theory. Biophysical Journal 61: 1616-1629 (1992).
71. Fields, G.B., D.O.V. Alonso, D. Stigter, and K.A. Dill. Theory for the Aggregation of Proteins and Copolymers. Journal of Physical Chemistry 96: 3974-3981 (1992). (PDF)
72. Stickle, D.F., L.G. Presta, K.A. Dill, and G.D. Rose. Hydrogen Bonding in Globular Proteins. Journal of Molecular Biology 226: 1143-1159 (1992).
73. Chan, H.S. and K.A. Dill. The Protein Folding Problem. Physics Today 46: 4-32 (1993).
Reprinted in Japanese in Parity, The Japanese Physical Science Magazine, December 1993, pp. 24-35.
74. Dill, K.A., K.M. Fiebig, and H.S. Chan. Cooperativity in Protein-Folding Kinetics. Proceedings of the National Academy of Sciences USA 90: 1942-1946 (1993).
75. Dill, K.A. Folding Proteins: Finding a Needle in a Haystack. Current Opinion in Structural Biology 3: 99-103 (1993).
76. Fiebig, K.M. and K.A. Dill. Protein Core Assembly Processes. Journal of Chemical Physics 98: 3475-3487 (1993).
77. De Young, L.R., K.A. Dill, and A.L. Fink. Aggregation and Denaturation of Apomyoglobin in Aqueous Urea Solutions. Biochemistry 32: 3877-3886 (1993). (PDF)
78. Yee, D.P. and K.A. Dill. Families and the Structural Relatedness Among Globular Proteins. Protein Science 2: 884-899 (1993).
79. Stigter, D. and K.A. Dill. Theory for Protein Solubilities. Fluid Phase Equilibria 82: 237-249 (1993).
80. Baker, D., H.S. Chan, and K.A. Dill. Coordinate-Space Formulation of Polymer Lattice Cluster Theory. Journal of Chemical Physics 98: 9951-9962 (1993).
81. Thomas, P.D. and K.A. Dill. Local and Nonlocal Interactions in Globular Proteins, and Mechanisms of Alcohol Denaturation. Protein Science 2: 2050-2065 (1993).
82. Yue, K. and K.A. Dill. Sequence-Structure Relationships in Proteins and Copolymers. Physical Review E 48: 2267-2278 (1993).
83. Stigter, D. and K.A. Dill. Theory for Second Virial Coefficients of Short DNA. Journal of Physical Chemistry 97: 12995-12997 (1993).
84. Chan, H.S. and K.A. Dill. Energy Landscapes and the Collapse Dynamics of Homopolymers. Journal of Chemical Physics 99: 2116-2127 (1993).
85. De Young, L.R., A.L. Fink, and K.A. Dill. Aggregation of Globular Proteins. Accounts of Chemical Research 26: 614-620 (1993).
86. Lattman, E.E., K.M. Fiebig, and K.A. Dill. Modeling Compact Denatured States of Proteins. Biochemistry 33: 6158-6166 (1994).
87. Bromberg, S. and K.A. Dill. Side-Chain Entropy and Packing in Proteins. Protein Science 3: 997-1009 (1994).
88. Chan, H.S., and K.A. Dill. Transition States and Folding Dynamics of Proteins and Heteropolymers. Journal of Chemical Physics 100: 9238-9257 (1994).
89. Yee, D.P., H.S. Chan, T.F. Havel, and K.A. Dill. Does Compactness Induce Secondary Structure in Proteins? A Study of Poly-Alanine Chains Computed by Distance Geometry. Journal of Molecular Biology 241: 557-573 (1994).
90. Chan, H.S. and K.A. Dill. Solvation: Effects of Molecular Size and Shape. Journal of Chemical Physics 101: 7007-7026 (1994).
91. Dill, K.A. and K.M. Fiebig. Hydrophobic Zippers: A Conformational Search Strategy for Proteins. In Statistical Mechanics, Protein Structure, and Protein Substrate Interactions, p. 109. S. Doniach, ed. New York: Plenum Press, 1994.
92. Yue, K., K.M. Fiebig, P.D. Thomas, H.S. Chan, E.I. Shakhnovich, and K.A. Dill. A Test of Lattice Protein Folding Algorithms. Proceedings of the National Academy of Sciences USA 92: 325-329 (1995).
93. Dill, K.A. and D. Stigter. Modeling Protein Stability as Heteropolymer Collapse. Advances in Protein Chemistry 46: 59-104 (1995).
94. Yue, K. and K.A. Dill. Forces of Tertiary Structural Organization in Globular Proteins. Proceedings of the National Academy of Sciences USA 92: 146-150 (1995).
95. Dill, K.A., S. Bromberg, K. Yue, K.M. Fiebig, D.P. Yee, P.D. Thomas, and H.S. Chan. Principles of Protein Folding - A Perspective From Simple Exact Models. Protein Science 4: 561-602, 1995.
96. Chan, H.S., S. Bromberg, and K.A. Dill. Models of Cooperativity in Protein Folding. Philosophical Transactions of the Royal Society, London B 348: 61-70, 1995.
97. Stigter, D., and K.A. Dill. Theory for Radii and Second Virial Coefficients of Polymers. I. Highly Charged Polyelectrolytes. Macromolecules 28: 5325-5337, 1995.
98. Stigter, D., and K.A. Dill. Theory for Radii and Second Virial Coefficients of Polymers. II. Weakly Charged Polyelectrolytes. Macromolecules 28: 5338-5346, 1995.
99. Miller, D.W., and K.A. Dill. A Statistical Mechanical Model for Hydrogen Exchange in Globular Proteins. Protein Science 4: 1860-1873, 1995.
100. Chen, S.-J., and K.A. Dill. Statistical Thermodynamics of Double-Stranded Polymer Molecules. Journal of Chemical Physics 103: 5802-5813, 1995.
101. Dill, K.A., H.S. Chan, and K. Yue. The Protein Folding Problem: Searching Conformations of Compact Chain Molecules. Macromolecular Symposia 98: 615-617, 1995.
102. Sun, S., P.D. Thomas, and K.A. Dill. A Simple Protein Folding Algorithm Using a Binary Code and Secondary Structure Constraints. Protein Engineering 8: 769-778, 1995.
103. Krukowski, A.E., H.S. Chan, and K.A. Dill. An Exact Lattice Model of Complex Solutions: Chemical Potentials Depend on Solute and Solvent Shape. Journal of Chemical Physics 103: 10675-10688, 1995.
104. Sun, S., R. Brem, H.S. Chan, and K.A. Dill. Designing Amino Acid Sequences To Fold With Good Hydrophobic Cores. Protein Engineering 9: 1205-1213 (1995). (PDF)
105. Yue, K., and K.A. Dill. Folding Proteins With a Simple Energy Function and Extensive Conformational Searching. Protein Science 5: 254-261, 1996.
106. Chan, H.S., and K.A. Dill. A Simple Model of Chaperonin-Mediated Protein Folding. Proteins: Structure, Function, and Genetics 24: 345-351, 1996.
107. Chan, H.S., and K.A. Dill. Comparing Folding Codes for Proteins and Polymers. Proteins: Structure, Function, and Genetics 24: 335-344, 1996.
108. Thomas, P.D., and K.A. Dill. Statistical Potentials Extracted From Protein Structures: How Accurate Are They? Journal of Molecular Biology 257: 457-469, 1996.
109. Chen, S.-J., and K.A. Dill. Structures and Symmetries of Proteins: A Knot Theory Approach. Journal of Chemical Physics 104: 5964-5973 (1996).
110. Wallace, D.G., and K.A. Dill. Treating Sequence Dependence of Protein Stability in a Mean-Field Model. Biopolymers 39: 115-127 (1996).
111. Beutler, T.C., and K.A. Dill. A Fast Conformational Search Strategy for Finding Low Energy Structures of Model Proteins. Protein Science 5: 2037-2043 (1996).
112. Stigter, D., and K.A. Dill. Binding of Ionic Ligands to Polyelectrolytes. Biophysical Journal 71: 2064-2074 (1996).
113. Thomas, P.D., and K.A. Dill. An Iterative Method for Extracting Energy-Like Quantities from Protein Structures. Proceedings of the National Academy of Science USA 93: 11628-11633 (1996).
114. Dill, K.A. Great Organizing Principles. Current Biology 6: 1204 (1996).
115. Dill, K.A., and A.R. Fersht. Editorial overview: Folding and Binding. Current Opinion in Structural Biology 6: 1-2 (1996).
116. Dill, K.A., and H.S. Chan. From Levinthal to Pathways to Funnels: The "New View" of Protein Folding Kinetics. Nature Structural Biology 4: 10-19 (1997). (PDF)
117. Dill, K.A. Additivity Principles in Biochemistry. Minireview for The Journal of Biological Chemistry 272: 701-704 (1997).
118. Dill, K.A., A.T. Phillips, and J.B. Rosen. Molecular Structure Prediction by Global Optimization. In Developments in Global Optimization, pp. 217-234. I.M. Bomze, et al., eds. The Netherlands: Kluwer Academic Publishers, 1997.
119. Haymet, A.D.J., K.A.T. Silverstein, and K.A. Dill. Hydrophobicity Reinterpreted as "Minimization of the Entropy Penalty of Solvation." Faraday Discussion 103: 117-124 (1997).
120. Chan, H.S., and K.A. Dill. Solvation: How to Obtain Microscopic Energies from Partitioning and Solvation Experiments. Annual Review of Biophysics and Biomolecular Structure 26: 425-459 (1997). (PDF)
121. Dill, K.A., J.B. Rosen, and A.T. Phillips. Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function. Journal of Computational Biology 4: 227-239 (1997).
122. Miller, D.W., and K.A. Dill. Ligand Binding to Proteins: The Binding Landscape Model. Protein Science 6: 2166-2179 (1997).
123. Armand, P., K. Kirshenbaum, A. Falicov, R.L. Dunbrack, K.A. Dill, R.N. Zuckermann, and F.E. Cohen. Chiral N-substituted glycines can form stable helical conformations. Folding & Design 2: 369-375 (1997).
124. Chan, H.S., and K.A. Dill. Protein Folding in the Landscape Perspective: Chevron Plots and Non-Arrhenius Kinetics. Proteins: Structure, Function, and Genetics 30: 2-33 (1998).
125. Kirshenbaum, K., A.E. Barron, R.A. Goldsmith, P. Armand, E.K. Bradley, K.T.V. Truong, K.A. Dill, F.E. Cohen, and R.N. Zuckermann. Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure. Proceedings of the National Academy of Sciences USA 95: 4303-4308 (1998).
126. Armand, P., K. Kirshenbaum, R.A. Goldsmith, S. Farr-Jones, A.E. Barron, K.T.V. Truong, K.A. Dill, D.F. Mierke, F.E. Cohen, R.N. Zuckermann, and E.K. Bradley. NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains. Proceedings of the National Academy of Sciences USA 95: 4309-4314 (1998).
127. Silverstein, K.A.T., A.D.J. Haymet, and K.A. Dill. A simple model of water and the hydrophobic effect. Journal of the American Chemical Society 120: 3166-3175 (1998). (HTML)
128. DeVido, D.R., J.G. Dorsey, H.S. Chan, and K.A. Dill. Oil/Water Partitioning Has a Different Thermodynamic Signature When the Oil Solvent Chains Are Aligned Than When They Are Amorphous. Journal of Physical Chemistry B 102: 7272-7279 (1998).
129. Chen, Shi-Jie and K.A. Dill. Theory for the Conformational Changes of Double-Stranded Chain Molecules. Journal of Chemical Physics 109: 4602-4616 (1998).
130. Silverstein, K.A.T., K.A. Dill, and A.D.J. Haymet. Hydrophobicity in a Simple Model of Water: Solvation and Hydrogen Bond Energies. Fluid Phase Equilibria 150-151: 83-90 (1998).
131. Tang, K.E.S. and K.A. Dill. Native Protein Fluctuations: The Conformational-Motion Temperature and the Inverse Correlation of Protein Flexibility with Protein Stability. Journal of Biomolecular Structure & Dynamics 16: 397-411 (1998). (PDF)
132. Ishikawa K., K. Yue, and K.A. Dill. Predicting the Structures of 18 Peptides Using Geocore. Protein Science 8: 716-721 (1999).
133. Brem, R., and K.A. Dill. The Effect of Multiple Binding Modes on Empirical Modeling of Ligand Docking to Proteins. Protein Science 8: 1134-1143 (1999).
134. Dill, K.A. Polymer Principles and Protein Folding. Protein Science 8: 1166-1180 (1999). (PDF)
135. Dill, K.A. Strengthening Biomedicine’s Roots. Nature 400: 309-310 (1999).
136. Kirshenbaum, K., R.N. Zuckermann, and K.A. Dill. Designing Polymers that Mimic Biomolecules. Current Opinion in Structural Biology 9: 530-535 (1999).
137. Silverstein, K.A.T., A.D.J. Haymet, and K.A. Dill. Molecular Model of Hydrophobic Solvation. Journal of Chemical Physics 111: 8000-8009 (1999).
138. Tang, K.E.S., and K.A. Dill. How Experiments See Fluctuations of Native Proteins: Perspective from an Exact Model. International Journal of Quantum Chemistry 75: 147-164 (1999). (PDF)
139. Foreman, K.W., A.T. Phillips, J.B. Rosen, and K.A. Dill. Comparing Search Strategies for Finding Global Optima on Energy Landscapes. Journal of Computational Chemistry 20: 1527-1532 (1999).
140. Young, M., K. Kirshenbaum, K.A. Dill, and S. Highsmith. Predicting Conformational Switches in Proteins. Protein Science 8: 1752-1764 (1999).
141. Dill, K.A., J. Deisenhofer, G.R. Fleming, H. Frauenfelder, K. Gerwert, J.A. McCammon, and H. Michel. Group Report: What Do We Need to Know About Proteins and Nucleic Acids? In Simplicity and Complexity in Proteins and Nucleic Acids. Edited by H. Frauenfelder, J. Deisenhofer, and P.G. Wolynes. Dahlem University Press, 1999.
142. Erman, B., and K.A. Dill. Gaussian Model of Protein Folding. Journal of Chemical Physics 112: 1050-1056 (2000).
143. Urbic, T., V. Vlachy, Yu.V. Kalyuzhnyi, N.T. Southall, and K.A. Dill. A Two-Dimensional Model of Water: Theory and Computer Simulations. Journal of Chemical Physics 112: 2843-2848 (2000).
144. Chen, S.-J., and K.A. Dill. RNA Folding Energy Landscapes. Proceedings of the National Academy of Sciences USA 97: 646-651 (2000).
145. Southall, N.T., and K.A. Dill. The Mechanism of Hydrophobic Solvation Depends on Solute Radius. Journal of Physical Chemistry B 104: 1326-1331 (2000). (PDF)
146. Brem, R., H.S. Chan, and K.A. Dill. Extracting microscopic energies from oil-phase solvation experiments. The Journal of Physical Chemistry B 104: 7471-7482 (2000). (PDF) (HTML)
147. Silverstein, K.A.T., A.D.J. Haymet, and K.A. Dill. The Strength of Hydrogen Bonds in Liquid Water and Around Nonpolar Solutes. Journal of the American Chemical Society 122: 8037-8041 (2000). (PDF)
148. Yue, K., and K.A. Dill. Constraint-Based Assembly of Tertiary Protein Structures from Secondary Structure Elements. Protein Science 9: 1935-1946 (2000).
149. Wang, T., J. Miller, N.S. Wingreen, C. Tang, and K.A. Dill. Symmetry and Designability for Lattice Protein Models. Journal of Chemical Physics 113: 8329-8336 (2000).
150. Rosen, J.B., A.T. Phillips, S.Y. Oh, and K.A. Dill. A Method for Parameter Optimization in Computational Biology. Biophysical Journal 79: 2818-2824 (2000).
151. Phillips, A.T., J.B. Rosen, and K.A. Dill. Energy Landscape Projections of Molecular Potential Functions. Nonconvex Optimization and Its Applications. C.A. Floudas and P.M. Pardalos, eds. Kluwer Academic Publishers, 47-55 (2000).
152. Southall, N.T., and K.A. Dill. Response to “Comment on ‘The Mechanism of Hydrophobic Solvation Depends on Solute Radius,’ J. Phys. Chem. B 2000, 104, 1326” Journal of Physical Chemistry B 105: 2082-2083 (2001). (PDF)
153. Tostesen, Eivind, Shi-Jie Chen, and Ken A. Dill. RNA Folding Transitions and Cooperativity. Journal of Physical Chemistry B 105: 1618-1630 (2001). (PDF)
154. Liang, Jie, and Ken A. Dill. Are Proteins Well-Packed? Biophysical Journal 81: 751-766 (2001).
155. Phillips, A.T., J.B. Rosen, and K.A. Dill. Convex Global Underestimation for Molecular Structure and Prediction. In Local To Global Optimization, P.M. Pardalos, et al., eds. Kluwer Academic Publishers, 1-18, 2001.
156. Kalyuzhnyi, Y.V., Vojko Vlachy, and Ken A. Dill. Hydration of Simple Ions. Effect of the Charge Density. Acta. Chim. Slov. 48: 309-316 (2001).
157. Ozkan, S.B., I. Bahar, and Ken A. Dill. Transition States and the Meaning of f-Values in Protein Folding Kinetics. Nature Structural Biology 8: 765-769 (2001).
158. Zhou, H.-X., and K.A. Dill. Stabilization of Proteins in Confined Spaces. Biochemistry 40: 11289-11293 (2001).
159. Kevin A. T. Silverstein, Ken A. Dill, A.D.J. Haymet. Hydrophobicity in a simple model of water: Entropy penalty as a sum of competing terms via full, angular expansion. Journal of Chemical Physics 114(4): 6303-6314 (2001). (PDF)
160. Erkip, A., B. Erman, C. Seok, and K.A. Dill. Parameter Optimization for the Gaussian model of protein folding. Polymer 43: 495-501 (2002). (PDF)
161. Ball, K.D., B. Erman, and K.A. Dill. The Elastic Net Algorithm and Protein Structure Prediction. Journal of Computational Chemistry 23: 77-83 (2002). (PDF)
162. Urbic, T., V. Vlachy, Yu.V. Kalyuzhnyi, N.T. Southall, and K.A. Dill. A Two-Dimensional Model of Water: Solvation of Nonpolar Solutes. Journal of Chemical Physics 116: 723-729 (2002).
163. Southall, N.T., K.A. Dill, and A.D.J. Haymet. A View of the Hydrophobic Effect. Journal of Physical Chemistry B 106: 521-533 (2002). (PDF)
164. Truskett, T.M., and K.A. Dill. Predicting Water’s Phase Diagram and Liquid-State Anomalies. Journal of Chemical Physics 117: 5101-5104 (2002). (PDF)
165. Ozkan, S.B., K.A. Dill, and I. Bahar. Fast-Folding Protein Kinetics, Hidden Intermediates, and the Sequential Stabilization Model. Protein Science 11: 1958-1970 (2002). (PDF)
166. Hribar, B., N.T. Southall, V. Vlachy, and K.A. Dill. How ions affect the structure of water. Journal of the American Chemical Society 124(41): 12302-12311 (2002). (PDF) (HTML)
167. Seok, C., J.B. Rosen, J.D. Chodera, and K.A. Dill. MOPED: Method for Optimizing Physical Energy Parameters Using Decoys. Journal of Computational Chemistry 24: 89-97 (2002). (PDF)
168. Truskett, T.M., and K.A. Dill. A Simple Statistical Mechanical Model of Water. Journal of Physical Chemistry B 106: 11829-11842 (2002). (PDF)
169. Southall, N.T., and K.A. Dill. Potential of Mean Force Between Two Hydrophobic Solutes in Water. Biophysical Chemistry 101--102: 295-307 (2002). (PDF)
170. Ozkan, S. Banu, K.A. Dill, and I. Bahar. Computing the Transition State Populations in Simple Protein Models. Biopolymers 68(1): 35-46 (2003). (PDF)
171. Weikl, T.R., and K.A. Dill. Folding Rates and Low-entropy-loss Routes of Two-state Proteins. Journal of Molecular Biology 329(3): 585-598 (2003). (PDF)(HTML)
172. Urbic, T., V. Vlachy, Y.V. Kalyuzhnyi, and K.A. Dill. Orientation-dependent Integral Equation Theory for a Two-dimensional Model of Water. Journal of Chemical Physics 118: 5516 (2003). (PDF)
173. Weikl, T.R., and K.A. Dill. Folding Kinetics of Two-state Proteins: Effect of Circularization, Permutation, and Crosslinks. Journal of Molecular Biology 332(4): 953-963 (2003). (PDF)
174. Schonbrun, J., and K.A. Dill. Fast Protein Folding Kinetics. Proceedings of the National Academy of Sciences USA 100(22): 12678-12682 (2003). (PDF)
175. Wu, C.W., K. Kirschenbaum, T.J. Sanborn, J.A. Patch, K. Huang, K.A. Dill, R.N. Zuckermann, and A.E. Barron. Structural and Spectroscopic Studies of Peptoid Oligomers with a-Chiral Aliphatic Side Chains. Journal of the American Chemical Society 125: 13525-13530 (2003). (PDF)
176. Lucas, A. and K.A. Dill. Statistical mechanics of pseudoknot polymers Journal of Chemical Physics 119(4): 2414-2421 (2003). (PDF)
177. E.A. Coutsias, C. Seok, M.P. Jacobson, and K.A. Dill. A Kinematic View of Loop Closure Journal of Computational Chemistry 25: 510-528 (2004). (PDF) (Code)
178. Thomas Horn, Byoung-Chul Lee, Ken A. Dill, and Ronald N. Zuckermann. Incorporation of Chemoselective Functionalities into Peptoids via Solid-Phase Submonomer Synthesis Bioconjugate Chemistry 15: 428--435 (2004). (PDF) (Supporting Docs)
179. Thomas R. Weikl, Matteo Palassini, Ken A. Dill. Cooperativity in 2-state Protein Folding Kinetics. Protein Science 13(3): 822-829 (2004). (PDF)
180. V. Vlachy, B. Hribar-Lee, Yu.V. Kalyuzhnyi, Ken A. Dill. Short-range interactions: from simple ions to polyelectrolyte solutions. Current Opinion in Colloid and Interface Science, Elsevier, 9 : 128-132 (2004). (PDF)
181. T. Urbic, V. Vlachy, O. Pizio, Ken A. Dill. Water-like fluid in the presence of Lennard-Jones obstacles: predictions of an associative replica Ornstein-Zernike theory. Journal of Molecular Liquids, 112 : 71-80 (2004). (PDF)
182. Evangelos A. Coutsias, Chaok Seok, Ken A. Dill. Using quaternions to calculate RMSD. Journal of Computational Chemistry, 25 : 1849-1857 (2004). (PDF) (Code)
183. Ken A. Dill, T. Truskett, V. Vlachy, B. Hribar-Lee. Modeling water, the hydrophobic effect, and ion solvation. Annual Review of Biophysics & Biomolecular Structure, 34 : 173-199 (2005). (PDF)
184. Bosco K. Ho, Evangelos A. Coutsias, Chaok Seok, Ken A. Dill. The flexibility in the Proline ring couples to the protein backbone. Protein Science. 14 : 1011-1018 (2005). (PDF)
185. Sheila S. Jaswal, Stephanie M.E. Truhlar, Ken A. Dill and David A. Agard. Comprehensive Analysis of Protein Folding Activation Thermodynamics Reveals a Universal Behavior Violated by Kinetically Stable Proteases. Journal of Molecular Biology, 347 (2): 355-366 (2005). (PDF)
186. Claudia Merlo, Ken A. Dill, and Thomas R. Weikl. $\Phi$ Values in protein-folding kinetics have energetic and structural components. PNAS, 102 (29): 10171--10175 (2005). (PDF)
187. Byoung-Chul Lee, Ronald N. Zuckermann, and Ken A. Dill. Folding a Nonbiological Polymer into a Compact Multihelical Structure. Journal of American Chemical Society, 127 : 10999--11009 (2005). (PDF) (Supplement PDF)
188. H. Xu and K.A. Dill. Water's Hydrogen Bonds in the Hydrophobic Effect: A Simple Model. Journal of Physical Chemistry B, 109 (49): 23611--7 (2005). (PDF)
189. I. Chorny, K.A. Dill, M.P. Jacobson. Surfaces Affect Ion Pairing. Journal of Physical Chemistry 109 (50): 24056--60 (2005). (PDF)
190. Evangelos A. Coutsias, Chaok Seok, Michael J. Wester, and Ken A. Dill. Resultants and Loop Closure. International Journal of Quantum Chemistry 106 : 176-189 (2006). (PDF) (Html and PDF)
191. David Chaing, Aravind K. Joshi, and Ken A. Dill. A grammatical theory for the conformational changes of simple helix bundles. Journal of Computational Biology 13 : 21-42 (2006). (PDF)
192. K. Ghosh, K.A. Dill, M.M. Inamdar, E. Seitaridou, and R. Phillips. Teaching the principles of statistical dynamics. American Journal of Physics 74 (2): 123--133 (2006). (PDF) (Html and PDF)
193. B.K. Ho and K.A. Dill. Folding very short peptides using molecular dynamics. PLOS Computational Biology 2 (4): 1--10 (2006). (View PDF) (Print PDF)
194. B.K. Ho and K.A. Dill. Correction: Folding very short peptides using molecular dynamics. PLOS Computational Biology 2 (5): 476--477 (2006). (PDF)
195. T. Urbic, V. Vlachy, and K.A. Dill. Confined water: a Mercedes-Benz model study. Journal of Physical Chemistry B., Condens Matter Surf Interfaces Biophys. 110 (10): 4963--70 (2006). (PDF)
196. D.L. Mobley, J.D. Chodera, and K.A. Dill. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. Journal of Chemical Physics 125 (8): 084902 (2006). (PDF)
197. B. Hribar-Lee and K.A. Dill. Modeling Simple Alcohols in Two Dimensions. Acta Chimica Slovenica 53 : 257--263 (2006). (PDF)
198. J.D. Chodera, W.C. Swope, J.W. Pitera, K.A. Dill. Long-time protein folding dynamics from short-time molecular dynamics simulations. Multiscale Modeling & Simulation 5 (4): 1214--1226 (2006). (Postprint) (PDF)
199. J.D. Chodera, W.C. Swope, J.W. Pitera, C. Seok, and K.A. Dill. Use of the weighted histogram analysis method for the analysis of simualted and parallel tempering simulations. Journal of Chemical Theory and Computation, 3: 26--41 (2007). (PDF) (Supplementary Material PDF) (Code)
200. J. Hockenmaier, A.K. Joshi, K.A. Dill. Routes are trees: The parsing perspective on protein folding. Proteins: Structure, Function, and Bioinformatics. 66 : 1--15 (2007). (PDF) (HTML)
201. T.R. Weikl and K.A. Dill. Transition states in protein-folding kinetics: the structural interpretation of Phi values. Journal of Molecular Biology 365 : 1578--1586 (2007). (PDF)
202. D.L. Mobley, E. Dumont, J.D. Chodera, and K.A. Dill Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. Journal of Physical Chemistry B 111 : 2242-2254 (2007). (PDF)
203. E. Seitaridou, M.M. Inamdar, R. Phillips, K. Ghosh, and K.A. Dill Measuring flux distributions for diffusion in the small-numbers limit. Journal of Physical Chemistry B 111 : 2288--2292 (2007). (PDF)
204. V.A. Voelz and K.A. Dill Exploring zipping and assembly as a protein folding principle. Proteins: Structure Function and Bioinformatics 66 (4):877--888 (2007). (PDF)
205. K.A. Dill, A. Lucas, J. Hockenmaier, L. Huang, D. Chiang, and A. Joshi. Computational Linguistics: a new tool for exploring biopolymer structures and statistical mechanics. Polymer 48 : 4289--4300 (2007). (PDF)
206. J.A. Bradford and K.A. Dill. Stochastic innovation as a mechanism by which catalysts might self-assembleinto chemical reaction networks. Proceedings of the National Academy of Sciences 104 (24): 10098--10103 (2007). (PDF)
207. J.D. Chodera, N. Singhal, V.S. Pande, K.A. Dill, and W.C. Swope. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. Journal of Chemical Physics 126 : 155101 (2007). (PDF)
208. K.A. Dill, S. Banu Ozkan, T.R.Weikl, J.D. Chodera and V.A. Voelz. The protein folding problem: when will it be solved?. Current Opinion in Structural Biology 17 : 342--346 (2007). (PDF)
209. S. Banu Ozkan, G. Albert Wu, J.D. Chodera and K.A. Dill. Protein folding by zipping and assembly. Proceedings of the National Academy of Sciences 104 (29): 11987--11992 (2007). (PDF)
210. D.L. Mobley, A.P. Graves, J.D. Chodera, A.C. McReynolds, B.K. Shoichet and K.A. Dill. Predicting absolute ligand binding free energies to a simple model site. Journal of Molecular Biology 371 (4): 1118--1134 (2007). (PDF)
211. A. Lucas, L. Huang, A. Joshi and K.A. Dill. Statistical mechanics of helix bundles using a dynamic programming approach. Journal of the American Chemical Society 129 : 4272--4281 (2007). (PDF)
212. A. Bizjak, T. Urbic, V. Vlachy, and K.A. Dill. The three-dimensional "Mercedes Benz" model of water. Acta Chimica Slovenica 54 : 532--537 (2007). (PDF)
213. D. L. Mobley, J. D. Chodera, and K. A. Dill. Confine and Release: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. Journal of Chemical Theory and Computation 3 (4): 1231-1235 (2007). (PDF)
214. T. Urbic, V Vlachy, Y. V. Kalyuzhnyi, and K. A. Dill. Theory for the solvation of nonpolar solutes in water. Journal of Chemical Physics 127 : 174505 (1-9) (2007). (PDF)
215. T. Urbic, V Vlachy, Y. V. Kalyuzhnyi, and K. A. Dill. An improved thermodynamic perturbation theory for Mercedes-Benz water. Journal of Chemical Physics 127 : 174511 (1-4) (2007). (PDF)
216. K. Ghosh, S. B. Ozkan, and K. A. Dill. The ultimate speed limit to protein folding is conformational searching. Journal of the American Chemical Society 129 : 11920--11927 (2007). (PDF)
217. D. L. Mobley, J. D. Chodera, and K. A. Dill. Treating entropy and conformational changes in implicit solvent simulations of small molecules. Journal of Physical Chemistry B 112(3) : 938--946 (2008). (PDF) (doi)
218. D. L. Mobley, A.E. Barber II, C. J. Fennell, and K. A. Dill. Charge asymmetries in hydration of polar solutes. Journal of Physical Chemistry B 112 : 2405--2414 (2008). (PDF) (doi)
219. K. A. Dill, S. B. Ozkan, M. S. Shell, and T. R. Weikl. The protein folding problem. Annu. Rev. Biophys. 37 : 289--316 (2008). (PDF)
220. G. Stock, K Ghosh, and K. A. Dill. Maximum Caliber: A variational approach applied to two-state dynamics. J. Chem. Phys. 128 (19): 194102 (2008). (PDF)
221. Tjasa Urbic, Tomaz Urbic, F. Avbelj, and K. A. Dill. Molecular simulations find stable structures in fragments of Protein G. Acta Chim. Slov. 55 : 385--395 (2008). (PDF)
222. Byoung-Chul Lee, T.K. Chu, K. A. Dill, and R. N. Zuckermann. Biomimetic Nanostructures: Creating a high-affinity Zinc-binding site in a folded nonbiological polymer. Journal of the American Chemical Society 130 : 8847--8855 (2008). (PDF PDF with links)
223. G. Albert Wu, E. A. Coutsias, K. A. Dill. Iterative Assembly of Helical Proteins by Optimal Hydrophobic Packing. Structure 16 : 1257--1266 (2008). (PDF)
224. M. S. Shell, R. Ritterson, K. A. Dill. A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation. J. Phys. Chem. B 112 : 6878--6886 (2008). (PDF)
225. V. A. Voelz, M. S. Shell, K. A. Dill. Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments. PLOS Computational Biology 5 (2): e1000281, 1--12 (2009). (PDF)
226. B. Hribar-Lee, V. Vlachy, K. A. Dill. Modeling Hofmeister Effects. Acta Chim. Slov. 56 : 196 -- 202 (2009). (PDF)
227. D. L. Mobley and K. A. Dill. Binding of Small-Molecule Ligands to Proteins: "What You See" Is Not Always "What You Get". Structure 17 : 489 -- 498 (2009). (PDF)
228. K. Ghosh and K. A. Dill. Theory for Protein folding cooperativity: Helix Bundles. Journal of the American Chemical Society 131 (6): 2306--2312 (2009). (PDF)
229. M. S. Shell, S. B. Ozkan, V. Voelz, G. A. Wu, and K. A. Dill. Blind Test of Physics-Based Prediction of Protein Structures. Biophysical Journal 96 : 917--924 (2009). (PDF)
230. D. L. Mobley, C. L. Bayly, M. D. Cooper, M. R Shirts, and K. A. Dill. Small molecule hydration free energies in explicit solvent: an extensive test of fixed-charge atomistic simulations. Journal of Chemical Theory and Computation 5 : 350--358 (2009). (PDF)
231. C. J. Fennell, A. Bizjak, V Vlachy, and K. A. Dill. Ion pairing in molecular simulations of aqueous alkali halide solutions. J. Phys. Chem. B 113 : 6782--6791 (2009). (PDF)
232. D. Wu, K. Ghosh, M. Inamdar, H. J. Lee, S. Fraser, K. A. Dill, and R. Phillips. Trajectory approach to two-state kinetics of single particles on sculpted energy langscapes Physical Review Letters 103 (5): 050603(1-4) (2009). (PDF)
233. K. Ghosh and K. A. Dill. Computing protein stabilities from their chain lengths. Proceedings of the National Academy of Sciences 106 (26): 10649--10654 (2009). (PDF)
234. M. Cruchok, V. Vlachy, and K. A. Dill. Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides. J. Chem. Phys. 130 : 134903 (2009). (PDF)
235. C. J. Fennell, A. Bizjak, V Vlachy, and K. A. Dill, S Sarupria, S Rajamani, and S Garde. Additions and Corrections to Ion pairing in molecular simulations of aqueous alkali halide solutions. J. Phys. Chem. B 113 : 14837--14838 (2009). (PDF)
236. S. E. Boyce, D. L. Mobley, G. J. Rocklin, A. P. Graves, K. A. Dill, and B. K. Shoichet. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J. Mol. Biol. doi:10.1016 / j.jmb.2009.09.049 (2009). (PDF)
237. A. Bizjak, T. Urbic, V. Vlachy, and K. A. Dill. Theory for the three-dimensional Mercedes-Benz model of water. J. Chem. Phys. 131 194504 1--7 (2009). (PDF)