Research Topics
| KENNETH A DILLSummaryAffiliation: University of California Country: USA Publications
| Collaborators
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Detail Information
Publications
From Levinthal to pathways to funnelsK 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...- 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... - Modeling water, the hydrophobic effect, and ion solvationKen 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... 
The protein folding problemKen A Dill
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
Annu Rev Biophys 37:289-316. 2008....- Polymer principles and protein foldingK 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... - Protein structure and energy landscape dependence on sequence using a continuous energy functionK 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... - Cooperativity in two-state protein folding kineticsThomas 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... - On the use of orientational restraints and symmetry corrections in alchemical free energy calculationsDavid 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... - Treating entropy and conformational changes in implicit solvent simulations of small moleculesDavid 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... - The ultimate speed limit to protein folding is conformational searchingKingshuk 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... - Exploring zipping and assembly as a protein folding principleVincent 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... - Protein folding by zipping and assemblyS 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... - The flexibility in the proline ring couples to the protein backboneBosco 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... - Ion pairing in molecular simulations of aqueous alkali halide solutionsChristopher 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.... - The elastic net algorithm and protein structure predictionKeith 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... - Charge asymmetries in hydration of polar solutesDavid 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... - Folding rates and low-entropy-loss routes of two-state proteinsThomas 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... - Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinksThomas 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... - Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamicsJohn D Chodera
Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
J Chem Phys 126:155101. 2007.... - Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solventDavid 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... - Folding very short peptides using molecular dynamicsBosco 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... - Surfaces affect ion pairingIlya 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... - Fast protein folding kineticsJack Schonbrun
Graduate Group in Biophysics, University of California, San Francisco, CA 94118, USA
Proc Natl Acad Sci U S A 100:12678-82. 2003.... - Assessment of the protein-structure refinement category in CASP8Justin L MacCallum
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, USA
Proteins 77:66-80. 2009.... - Blind test of physics-based prediction of protein structuresM 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... - Iterative assembly of helical proteins by optimal hydrophobic packingG 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... - Water's hydrogen bonds in the hydrophobic effect: a simple modelHuafeng 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... - MOPED: method for optimizing physical energy parameters using decoysChaok 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... - Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical reaction networksJustin 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... - Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteasesSheila 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... - Predicting absolute ligand binding free energies to a simple model siteDavid 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... - The stabilities of protein crystalsJeremy 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... - Folding a nonbiological polymer into a compact multihelical structureByoung-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... - Potential of mean force between two hydrophobic solutes in waterNoel 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... - Predicting ligand binding affinity with alchemical free energy methods in a polar model binding siteSarah 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... - Oil/water transfer is partly driven by molecular shape, not just sizeChristopher 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.... - Nonuniversal power law scaling in the probability distribution of scientific citationsGeorge 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...