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Principal Investigator/Program Director (Last, First, Middle): |
Dill, Ken A. |
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BIOGRAPHICAL SKETCHProvide the following information for the key
personnel and other significant contributors in the order listed on Form Page
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NAME Ken A. Dill |
POSITION TITLE Professor |
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eRA COMMONS USER NAME kadill |
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EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) |
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INSTITUTION AND LOCATION |
DEGREE (if
applicable) |
YEAR(s) |
FIELD OF STUDY |
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MIT, Cambridge, MA |
S.B., S.M. |
1971 |
Mechanical Engineering |
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UCSD, La Jolla, CA (with BH Zimm) |
Ph.D. |
1978 |
Biology |
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Stanford, Palo Alto, CA (with PJ Flory) |
Postdoc |
1981 |
Chemistry |
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Professional Experience:
2001 - Associate
Dean, Research, School of Pharmacy, UCSF
1989 - Professor,
Pharmaceutical Chemistry, Biochem/Biophysics, Biopharmaceutics, UCSF.
1989 - Adjunct
Professor, Pharmaceutics, U. Utah.
1996 - Faculty
Biochemist, Lawrence Berkeley National Lab.
1985 - 1989 Associate
Professor, Pharmaceutical Chemistry, UCSF.
1985 – 1989 Associate
Adjunct Professor, U. Utah.
1982 – 1985 Assistant
Professor, UCSF.
1981 – 1982 Assistant
Professor, Chemistry, U. Florida, Gainesville.
Service:
Biophysical
Society (President 1998, Council 1992-95, Executive Committee 1992, Chair,
Public Affairs 2001-2007, Nominating Committee chair 1993). NIBIB Review Board
on Intramural Activities, 2004.
Acting Director, UCSF Biophysics Program 1994-95. Co-chair 1993 Gordon
Conference on Proteins. Co-organizer 1990 AAAS Symposium on Protein Folding.
National Research Council: Polymer Science & Engineering, Õ92-Õ94;
Biomaterials & Processes, Õ05-Õ07.
Protein Society (Executive Committee, 2002-2005, Nominating Committee
chair 1994). BBCA study section, NIH (1997-2001; ad hoc, Ô93, Ô06). American
Physical Society, Physics Policy Committee, Ô03-Ô05; Division Biological
Physics Executive Committee Ô01–Ô04, Awards Committee Ô01–Ô04. Co-director BWF Graduate Program In
Quantitative Biology, UCSF. Founder & Director, Bridging the Sciences
Federal Initiative – a coalition of 15 basic research societies, 250,000
scientists, supporting deep innovation and the Life/Physical Sciences
interface.
Editorial/Advisory
Boards:
Current: Ann Rev Biophys & Biomol Structure, Protein Engineering,
Physical Biology, Multiscale Modeling & Simulation, Structure, Biopolymers,
Biophysical Chemistry, J. Molecular Recognition; Past: Protein Science, Ann Rev Physical Chemistry, Biophysical Journal, Theochem, Chemical Physics, Current
Biology.
Honors:
Member,
National Academy of Sciences (2008-).
Hans Neurath Award (Protein Society, 1998). Distinguished Service Award,
Biophysical Society (2007). Fellow, Institute of Physics (elected 2004);
Fellow, Biophysical Society (elected 2002); Fellow, AAAS (elected 1997);
Fellow, American Physical Society (elected 1991). Distinguished Teaching Award (UCSF) Academic Senate, (1987);
Joseph M. Long Foundation Prize for Excellence in Teaching, (UCSF, 1987). Pew Scholar (1985-1989). Damon
Runyon-Walter Winchell Postdoctoral Fellowship (1979-1980); National Science
Foundation Predoctoral Fellowship (1971-1974).
Lectures:
Gary
Griffin Lecture (University of New Orleans, 2008), Engbretsons Lecture (North
Dakota State University, 2006); Inaugural Harrison Shull Lecture, Chemistry
(Indiana U. 2004); Nieuwland-Reilly Lectures, Chemistry (Notre Dame, 2002);
Meloche Lecture, Chemistry (U. Wisconsin 2001); Norman Hascoe Lecture, Physics
(U. Conn., 1998); Harland G. Wood Lecture, Biochemistry, Case-Western Reserve
U, 1998; Clayton Foundation Regents Lectures, U. Texas, 1998; Keynote Lecture, Texas Folders
Meeting, 1997; Moses Gomberg Lecture, U. Michigan, 1997; National Lecture,
Biophysical Society 1996; Joseph F. Foster Lecture, Purdue 1996; C.B. Anfinsen
Lecture, Johns Hopkins Folding meeting 1996; Warren L. McCabe Lecture, NCSU,
1995; Jesse W. Beams Lectures, U. Virginia, 1993; Wesleyan Lectures, Wesleyan
1993; Merck Lecture, Purdue, 1992; Dartmouth Lectures, Dartmouth College 1991;
Bayer/Mobay Lecture, U. Pittsburgh, 1989.
Publications:
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).
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 (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).
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).
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).
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).
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).
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).
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 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
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).
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. The 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).
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).
135. Dill, K.A.
Strengthening BiomedicineÕs 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).
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 97: 646-651 (2000).
145. Southall, N.T., and
K.A. Dill. The Mechanism of Hydrophobic Solvation Depends on Solute
Radius. The Journal of Physical Chemistry B 104: 1326-1331 (2000).
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).
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).
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 ÒComment on ÔThe Mechanism of Hydrophobic
Solvation Depends on Solute Radius,Õ J. Phys. Chem. B 2000, 104, 1326Ó Journal
of Physical Chemistry B 105:
2082-2083 (2001).
153. Tostesen, Eivind,
Shi-Jie Chen, and Ken A. Dill. RNA Folding Transitions and Cooperativity.
Journal of Physical Chemistry B 105: 1618-1630 (2001).
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 Chimica Slovenica 48: 309-316 (2001).
157. Ozkan, S.B., I.
Bahar, and Ken A. Dill. Transition States and the Meaning of Phi-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: 6303-6314 (2001).
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).
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).
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).
164. Truskett, T.M., and
K.A. Dill. Predicting WaterÕs Phase Diagram and Liquid-State
Anomalies. Journal of Chemical Physics 117: 5101-5104 (2002).
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).
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: 12302-12311 (2002).
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).
168. Truskett, T.M., and
K.A. Dill. A Simple Statistical Mechanical Model of Water. Journal
of Physical Chemistry B 106:
11829-11842 (2002).
169. Southall, N.T., and
K.A. Dill. Potential of Mean Force Between Two Hydrophobic Solutes in
Water. Biophysical Chemistry 101: 295-307 (2002).
170. Ozkan, S. Banu,
K.A. Dill, and I. Bahar. Computing the Transition State Populations in
Simple Protein Models. Biopolymers 68: 35-46 (2003).
171. Weikl, T.R., and
K.A. Dill. Folding Rates and Low-Entropy-Loss Routes of Two-state
Proteins. Journal of Molecular Biology 329: 585-598 (2003).
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).
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: 953-963 (2003).
174. Schonbrun, J., and
K.A. Dill. Fast Protein Folding Kinetics. Proceedings of the
National Academy of Sciences USA 100: 12678-12682 (2003).
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).
176. Lucas, A. and K.A.
Dill. Statistical mechanics of pseudoknot polymers Journal of
Chemical Physics 119: 2414-2421 (2003).
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).
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).
179. Thomas R. Weikl,
Matteo Palassini, Ken A. Dill. Cooperativity in 2-state Protein Folding
Kinetics. Protein Science 13: 822-829 (2004).
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 9: 128-132 (2004).
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).
182. Evangelos A.
Coutsias, Chaok Seok, Ken A. Dill. Using quaternions to calculate RMSD.
Journal of Computational Chemistry 25: 1849-1857 (2004).
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).
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).
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: 355-366 (2005).
186. Claudia Merlo, Ken
A. Dill, and Thomas R. Weikl. Phi values in protein-folding kinetics have
energetic and structural components. Proceedings of the National
Academy of Sciences 102: 10171-10175 (2005).
187. Byoung-Chul Lee,
Ronald N. Zuckermann, and Ken A. Dill. Folding a Nonbiological Polymer
into a Compact Multihelical Structure. Journal of the American
Chemical Society 127: 10999-11009 (2005).
188. H. Xu and K.A.
Dill. Water's Hydrogen Bonds in the Hydrophobic Effect: A Simple
Model. Journal of Physical
Chemistry B 109: 23611-7 (2005).
189. I. Chorny, K.A.
Dill, M.P. Jacobson. Surfaces
Affect Ion Pairing. Journal of
Physical Chemistry B 109: 24056-60 (2005).
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).
191. David Chiang,
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).
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: 123-133 (2006).
193. B.K. Ho and K.A.
Dill. Folding very short peptides using molecular dynamics. PLOS Computational Biology 2: 1-10 (2006).
194. B.K. Ho and K.A.
Dill. Correction: Folding very short peptides using molecular dynamics.
PLOS Computational Biology 2: 476-477 (2006).
195. T. Urbic, V.
Vlachy, and K.A. Dill. Confined water: a Mercedes-Benz model study.
Journal of Physical Chemistry B 110: 4963-4970 (2006).
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: 084902
(2006).
197. B. Hribar-Lee and
K.A. Dill. Modeling Simple Alcohols in Two Dimensions. Acta
Chimica Slovenica 53: 257-263 (2006).
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: 1214-1226 (2006).
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 simulated and parallel tempering
simulations. Journal of Chemical Theory and Computation 3: 26-41 (2007).
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).
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).
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).
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).
204. V.A. Voelz and K.A.
Dill Exploring zipping and assembly as a protein folding principle.
Proteins: Structure, Function & Bioinformatics 66: 877-888 (2007).
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).
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: 10098-10103 (2007).
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).
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).
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: 11987-11992 (2007).
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: 1118-1134 (2007).
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).
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).
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: 1231-1235 (2007).
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 (2007).
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 (2007).
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).
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).
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).
219. K. A. Dill, S. B.
Ozkan, M. S. Shell, and T. R. Weikl.
The protein folding problem.
Annual
Reviews Biophysics 37: 289-316 (2008).