KENNETH A DILL

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint From Levinthal to pathways to funnels
    K A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco 94143 1204, USA
    Nat Struct Biol 4:10-9. 1997
  2. ncbi request reprint The protein folding problem: when will it be solved?
    Ken A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
    Curr Opin Struct Biol 17:342-6. 2007
  3. ncbi request reprint Modeling water, the hydrophobic effect, and ion solvation
    Ken A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143 2240, USA
    Annu Rev Biophys Biomol Struct 34:173-99. 2005
  4. pmc The protein folding problem
    Ken A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
    Annu Rev Biophys 37:289-316. 2008
  5. pmc Polymer principles and protein folding
    K A Dill
    University of California, San Francisco 94118, USA
    Protein Sci 8:1166-80. 1999
  6. ncbi request reprint Protein structure and energy landscape dependence on sequence using a continuous energy function
    K A Dill
    Department of Pharmaceutical Chemistry, University of California at San Francisco, 94118, USA
    J Comput Biol 4:227-39. 1997
  7. pmc Cooperativity in two-state protein folding kinetics
    Thomas R Weikl
    Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143, USA Thomas
    Protein Sci 13:822-9. 2004
  8. pmc On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
    David L Mobley
    Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143, USA
    J Chem Phys 125:084902. 2006
  9. pmc Treating entropy and conformational changes in implicit solvent simulations of small molecules
    David L Mobley
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
    J Phys Chem B 112:938-46. 2008
  10. ncbi request reprint The ultimate speed limit to protein folding is conformational searching
    Kingshuk Ghosh
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
    J Am Chem Soc 129:11920-7. 2007

Collaborators

Detail Information

Publications37

  1. ncbi request reprint From Levinthal to pathways to funnels
    K A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco 94143 1204, USA
    Nat Struct Biol 4:10-9. 1997
    ..At that point we hope to learn much more about the real shapes of protein folding landscapes...
  2. ncbi request reprint The protein folding problem: when will it be solved?
    Ken A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
    Curr Opin Struct Biol 17:342-6. 2007
    ..Even the once-challenging Levinthal puzzle now seems to have an answer--a protein can avoid searching irrelevant conformations and fold quickly by making local independent decisions first, followed by non-local global decisions later...
  3. ncbi request reprint Modeling water, the hydrophobic effect, and ion solvation
    Ken A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143 2240, USA
    Annu Rev Biophys Biomol Struct 34:173-99. 2005
    ..This review gives a perspective from simple models on how the physical properties of water-as a pure liquid and as a solvent-derive from the geometric and hydrogen bonding properties of water...
  4. pmc The protein folding problem
    Ken A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
    Annu Rev Biophys 37:289-316. 2008
    ....
  5. pmc Polymer principles and protein folding
    K A Dill
    University of California, San Francisco 94118, USA
    Protein Sci 8:1166-80. 1999
    ..Energy landscapes give a language for bridging between microscopics and macroscopics, for relating folding kinetics to equilibrium fluctuations, and for developing new and faster computational search strategies...
  6. ncbi request reprint Protein structure and energy landscape dependence on sequence using a continuous energy function
    K A Dill
    Department of Pharmaceutical Chemistry, University of California at San Francisco, 94118, USA
    J Comput Biol 4:227-39. 1997
    ..By using different starting points, we show that the method appears to find global minima. Since we can currently find stable states of 36-residue chains in 2.4 hours, the method may be practical for small proteins...
  7. pmc Cooperativity in two-state protein folding kinetics
    Thomas R Weikl
    Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143, USA Thomas
    Protein Sci 13:822-9. 2004
    ..The barrier to folding is the formation of predominantly local structures such as helices and hairpins, which are needed to bring nonlocal pairs of amino acids into contact...
  8. pmc On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
    David L Mobley
    Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143, USA
    J Chem Phys 125:084902. 2006
    ..Our method is easily parallelizable, well suited for cases where a ligand cocrystal structure is not available, and can utilize initial orientations generated by docking packages...
  9. pmc Treating entropy and conformational changes in implicit solvent simulations of small molecules
    David L Mobley
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
    J Phys Chem B 112:938-46. 2008
    ..03) with the number of rotatable bonds. The present study illustrates that implicit solvent modeling can be improved by eliminating the approximation that solutes are rigid...
  10. ncbi request reprint The ultimate speed limit to protein folding is conformational searching
    Kingshuk Ghosh
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
    J Am Chem Soc 129:11920-7. 2007
    ..We find that the upper estimate of the free energy barriers are positive but small, as little as 0.5 kT...
  11. ncbi request reprint Exploring zipping and assembly as a protein folding principle
    Vincent A Voelz
    Graduate Group in Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
    Proteins 66:877-88. 2007
    ..We find that the efficiency increases with chain length, although our range of chain lengths is limited. We believe these insights may be useful for developing faster protein conformational search algorithms...
  12. pmc Protein folding by zipping and assembly
    S Banu Ozkan
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 104:11987-92. 2007
    ..The present work also shows that physics-based force fields are quite good and that physics-based protein structure prediction may be practical, at least for some small proteins...
  13. pmc The flexibility in the proline ring couples to the protein backbone
    Bosco K Ho
    Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA 94148, USA
    Protein Sci 14:1011-8. 2005
    ..The strain in the C(gamma)-C(delta)-N angle appears to be the principal barrier between the UP and DOWN pucker. This strain is relaxed to allow the proline ring to flatten in the rare PLANAR conformation...
  14. pmc Ion pairing in molecular simulations of aqueous alkali halide solutions
    Christopher J Fennell
    Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143, USA
    J Phys Chem B 113:6782-91. 2009
    ....
  15. ncbi request reprint The elastic net algorithm and protein structure prediction
    Keith D Ball
    Department of Pharmaceutical Chemistry, University of California at San Francisco, 94118, USA
    J Comput Chem 23:77-83. 2002
    ..The computer time tau scales as tau approximately n, where n is the number of amino acids. This method may prove to be useful for structure refinement and prediction...
  16. pmc Charge asymmetries in hydration of polar solutes
    David L Mobley
    Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143, USA
    J Phys Chem B 112:2405-14. 2008
    ..These asymmetries are mainly enthalpic, arising primarily from the first solvation shell water structure. Such effects are not readily captured by implicit solvent models, which respond symmetrically with respect to charge...
  17. ncbi request reprint Folding rates and low-entropy-loss routes of two-state proteins
    Thomas R Weikl
    Department of Pharmaceutical Chemistry, University of California, Box 2240, San Francisco, CA 94143 2240, USA
    J Mol Biol 329:585-98. 2003
    ..This model indicates how much of protein folding may take place in parallel, not along a single reaction coordinate or with a single transition state...
  18. ncbi request reprint Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks
    Thomas R Weikl
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143 2240, USA
    J Mol Biol 332:953-63. 2003
    ..As a test of the model, we propose mutations that should reverse these outcomes...
  19. ncbi request reprint Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
    John D Chodera
    Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
    J Chem Phys 126:155101. 2007
    ....
  20. ncbi request reprint Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent
    David L Mobley
    Department of Pharmaceutical Chemistry and Graduate Group in Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
    J Phys Chem B 111:2242-54. 2007
    ..Further, we find that the discrepancy with experimental hydration free energies grows substantially with the polarity of the compound, as does its variation across theory levels...
  21. pmc Folding very short peptides using molecular dynamics
    Bosco K Ho
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
    PLoS Comput Biol 2:e27. 2006
    ..Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments...
  22. ncbi request reprint Surfaces affect ion pairing
    Ilya Chorny
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143 2240, USA
    J Phys Chem B 109:24056-60. 2005
    ..Such asymmetries are also not predicted by implicit solvent models. These results may be useful for improving computational models of solvation in biology and chemistry...
  23. pmc Fast protein folding kinetics
    Jack Schonbrun
    Graduate Group in Biophysics, University of California, San Francisco, CA 94118, USA
    Proc Natl Acad Sci U S A 100:12678-82. 2003
    ....
  24. pmc Assessment of the protein-structure refinement category in CASP8
    Justin L MacCallum
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, USA
    Proteins 77:66-80. 2009
    ....
  25. pmc Blind test of physics-based prediction of protein structures
    M Scott Shell
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
    Biophys J 96:917-24. 2009
    ..This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences...
  26. pmc Iterative assembly of helical proteins by optimal hydrophobic packing
    G Albert Wu
    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143 2240, USA
    Structure 16:1257-66. 2008
    ..It may be useful for protein structure prediction...
  27. ncbi request reprint Water's hydrogen bonds in the hydrophobic effect: a simple model
    Huafeng Xu
    Department of Pharmaceutical Chemistry and Graduate Group of Biophysics, University of California, San Francisco, San Francisco, California 94143, USA
    J Phys Chem B 109:23611-7. 2005
    ..It explains the puzzling experimental observation that dissolving a nonpolar solute in hot water has positive entropy...
  28. ncbi request reprint MOPED: method for optimizing physical energy parameters using decoys
    Chaok Seok
    Department of Pharmaceutical Chemistry, University of California in San Francisco, San Francisco, California 94118, USA
    J Comput Chem 24:89-97. 2003
    ..MOPED successfully finds improved parameters that allow EEF1 to discriminate native from decoy structures on all protein structures that do not have metals or prosthetic groups...
  29. pmc Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical reaction networks
    Justin A Bradford
    Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 104:10098-103. 2007
    ..This model may be useful for understanding organizational processes in prebiotic chemistry and for developing new kinds of self-organization in chemically reacting systems...
  30. ncbi request reprint Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases
    Sheila S Jaswal
    Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
    J Mol Biol 347:355-66. 2005
    ..Attaining such functional properties seems possible only through the gross perturbation of the folding thermodynamics, which in turn has required the co-evolution of pro regions as folding catalysts...
  31. pmc Predicting absolute ligand binding free energies to a simple model site
    David L Mobley
    Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143 2518, USA
    J Mol Biol 371:1118-34. 2007
    ..Finally, we examined the impact of holding the protein rigid, as in docking, with a view to learning how approximations made in docking affect accuracy and how they may be improved...
  32. pmc The stabilities of protein crystals
    Jeremy D Schmit
    Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158, USA
    J Phys Chem B 114:4020-7. 2010
    ..The model shows that the salting out phenomena is not due to more counterion shielding but to lowered counterion translational entropy. Models of this type may help guide faster and better ways to crystallize proteins...
  33. ncbi request reprint Folding a nonbiological polymer into a compact multihelical structure
    Byoung Chul Lee
    Graduate Group in Biophysics and Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, CA 94143, USA
    J Am Chem Soc 127:10999-1009. 2005
    ..We found that certain constructs fold up with a hydrophobic core and have cooperative folding transitions. Such molecules may ultimately provide a platform for designing specific functions resembling those of proteins...
  34. ncbi request reprint Potential of mean force between two hydrophobic solutes in water
    Noel T Southall
    Graduate Group in Biophysics, University of California at San Francisco, San Francisco, CA 94143 1204, USA
    Biophys Chem 101:295-307. 2002
    ..Contacts are stabilized by entropy, whereas solvent-separated solute pairing is stabilized by enthalpy. The free energy of interaction for small solutes is well-approximated by scaled-particle theory...
  35. pmc Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
    Sarah E Boyce
    Graduate Group in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA 94158 2518, USA
    J Mol Biol 394:747-63. 2009
    ..We believe that these results can help guide future improvements in physics-based absolute binding free energy methods...
  36. pmc Oil/water transfer is partly driven by molecular shape, not just size
    Christopher J Fennell
    Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143, USA
    J Am Chem Soc 132:234-40. 2010
    ....
  37. pmc Nonuniversal power law scaling in the probability distribution of scientific citations
    George J Peterson
    Biophysics Graduate Group, and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 107:16023-7. 2010
    ..The power-law exponent is not universal. Individuals who are highly cited have a systematically smaller exponent than individuals who are less cited...