Dill, Ken A. - Department of Pharmaceutical Chemistry, University of California at San Francisco

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Dill, Ken A. - Department of Pharmaceutical Chemistry, University of California at San Francisco

Transition-States in Protein Folding Kinetics: The Structural Interpretation of values
Feature Article Computational linguistics: A new tool for exploring biopolymer
A Simple Statistical Mechanical Model of Water Thomas M. Truskett, and Ken A. Dill
Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model
Trajectory Approach to Two-State Kinetics of Single Particles on Sculpted Energy Landscapes Kingshuk Ghosh,2
Routes Are Trees: The Parsing Perspective on Protein Folding
1980 J. Phys. Chem. 1987, 91, 1980-1988 are between 1.4 and 4.4 nm. Thus, the 7 nm of the effective
0 Copyright 1990 by the American Chemical Society Volume 29, Number 31 Perspectives in Biochemistry
5974 Biochemistry 1991, 30, 5974-5985 Milostone, L., Barton, D. E., Francke, U., & Broadus, A.
Protein Science (1995), 4:561-602. Cambridge University Press. Printed in the USA. Copyright 0 1995 The Protein Society
Protein Engineering vol.8 no.12 pp. 1205-1213, 1995 Designing amino acid sequences to fold with good hydrophobic
Polymer principles and protein folding KEN A. DILL1
The Elastic Net Algorithm and Protein Structure Prediction KEITH D. BALL,1
MOPED: Method for Optimizing Physical Energy Parameters Using Decoys
Computing the Transition State Populations in Simple
Folding Kinetics of Two-state Proteins: Effect of Circularization, Permutation, and Crosslinks
Cooperativity in two-state protein folding kinetics THOMAS R. WEIKL,1,2
Folding a Nonbiological Polymer into a Compact Multihelical Byoung-Chul Lee, Ronald N. Zuckermann,*, and Ken A. Dill*,,
Confined Water: A Mercedes-Benz Model Study T. Urbic, V. Vlachy, and K. A. Dill*,
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
MULTISCALE MODEL. SIMUL. c 2006 Society for Industrial and Applied Mathematics Vol. 5, No. 4, pp. 12141226
Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent
reaction networks Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical
Theory for the solvation of nonpolar solutes in water T. Urbic and V. Vlachy
Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules
Charge Asymmetries in Hydration of Polar Solutes David L. Mobley, Alan E. Barber II, Christopher J. Fennell, and Ken A. Dill*,
Maximum Caliber: A variational approach applied to two-state dynamics Gerhard Stock,1,a
Biomimetic Nanostructures: Creating a High-Affinity Zinc-Binding Site in a Folded Nonbiological Polymer
Subscriber access provided by -Access paid by the | UCSF Library Journal of the American Chemical Society is published by the American Chemical
196 Acta Chim. Slov. 2009, 56, 196202 Hribar-Lee et al.: Modeling Hofmeister Effects
Binding of Small-Molecule Ligands to Proteins: ``What You See'' Is Not Always ``What You Get''
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Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions Christopher J. Fennell,*,
ADDITIONS AND CORRECTIONS Christopher J. Fennell,* Alan Bizjak, Vojko Vlachy,
Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site
Oil/Water Transfer Is Partly Driven by Molecular Shape, Not Christopher J. Fennell,
A statistical mechanical theory for a two-dimensional model of water Tomaz Urbic1,a
Dynamical fluctuations in biochemical reactions and cycles S. Press,1
Receptacle Model of Salting-In by Tetramethylammonium Ions Barbara Hribar-Lee,*,
What Drives Amyloid Molecules To Assemble into Oligomers and Fibrils? Jeremy D. Schmit,
Modeling aqueous solvation with semi-explicit assembly
The Protein Folding Ken A. Dill,1,2
values in protein-folding kinetics have energetic and structural components
Folding Rates and Low-entropy-loss Routes of Two-state Proteins
Theory for the three-dimensional Mercedes-Benz model of water Alan Bizjak,1
Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering
RNA Folding Transitions and Cooperativity Eivind Tstesen, Shi-Jie Chen,*, and Ken A. Dill
Correction: Folding Very Short Peptides Using Molecular Dynamics Bosco K. Ho, Ken A. Dill
3974 J. Phys. Chem. 1992, 96, 3974-3981 Theory for the Aggregation of Proteins and Copolymerst
proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS HIGH ACCURACY ASSESSMENT
The Flexibility in the Proline Ring Couples to the Protein Backbone
Cellular Proteomes Have Broad Distributions of Protein Stability Kingshuk Ghosh
Statistical mechanics of pseudoknot polymers Adam Lucasa)
Protein folding by zipping and assembly S. Banu Ozkan*
Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
A grammatical theory for the conformational changes of simple helix bundles
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
Treating entropy and conformational changes in implicit solvent simulations of small molecules
John D. Chodera email jchodera@stanford.edu
Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments
Surfaces Affect Ion Pairing Ilya Chorny, Ken A. Dill,*, and Matthew P. Jacobson*,
Parameter optimization for the Gaussian model of protein foldingq Albert Erkipa
Hydrophobicity in a simple model of water: Entropy penalty as a sum of competing terms via full, angular expansion
3986 Macromolecules 1989,22, 3986-3997 1 6 1 8 2 2
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
257Acta Chim. Slov. 2006, 53, 257263 Hribar-Lee, and Dill Modeling Simple Alcohols in Two Dimensions
Measuring Flux Distributions for Diffusion in the Small-Numbers Limit Effrosyni Seitaridou, Mandar M. Inamdar, Rob Phillips,*,, Kingshuk Ghosh, and Ken Dill
385Acta Chim. Slov. 2008, 55, 385395 Urbi~ et al.: Molecular simulations find stable structures in fragments of Protein G
University of California Year 2007 Paper 2270
Teaching the principles of statistical dynamics Kingshuk Ghosh and Ken A. Dill
Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic
Chem. Rev. 1989, 89, 331-346 331 The Molecular Mechanism of Retention in Reversed-Phase Liquid
Receptacle Model of Salting-In by Tetramethylammonium Ions Barbara Hribar-Lee,*,
Nonuniversal power law scaling in the probability distribution of scientific citations
Fast protein folding kinetics Jack Schonbrun*
Blind Test of Physics-Based Prediction of Protein Structures M. Scott Shell,
Folding Very Short Peptides Using Molecular Dynamics
Confine-and-Release Method: Obtaining Correct Binding Free Energies in the
COMMUNICATIONS Predicting water's phase diagram and liquid-state anomalies
Supporting Information Folding a Non-biological Polymer into a Compact
Statistical Mechanics of Helix Bundles Using a Dynamic Programming Approach
Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. Supplementary material: Sample Implementation in Fortran 95
Incorporation of Chemoselective Functionalities into Peptoids via Solid-Phase Submonomer Synthesis
How Ions Affect the Structure of Water Barbara Hribar, Noel T. Southall, Vojko Vlachy, and Ken A. Dill*,
A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation M. Scott Shell*
Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides
An Alternative Explanation for the Catalytic Proficiency of Orotidine 5-Phosphate Decarboxylase
How Experiments See Fluctuations of Native Proteins: Perspective from an
532 Acta Chim. Slov. 2007, 54, 532537 Bizjak et al.: The ThreeDimensional "Mercedes Benz" Model of Water
BIOPHYSICSAND COMPUTATIONALBIOLOGY
Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent
The protein folding problem: when will it be solved? Ken A Dill1
The Ultimate Speed Limit to Protein Folding Is Conformational Kingshuk Ghosh, S. Banu Ozkan, and Ken A. Dill*
Alchemical Free Energy Calculations: Ready for Prime Time?
Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering
FEATURE ARTICLE A View of the Hydrophobic Effect
Supporting Information Incorporation of Chemoselective Functionalities
An improved thermodynamic perturbation theory for Mercedes-Benz water and V. Vlachy
J Stat Phys DOI 10.1007/s10955-011-0232-9
Published: April 27, 2011 r 2011 American Chemical Society 6202 dx.doi.org/10.1021/jp111112s |J. Phys. Chem. B 2011, 115, 62026212
THE JOURNAL OF CHEMICAL PHYSICS 135, 085103 (2011) Electrostatics and aggregation: How charge can turn a crystal into a gel
THE PROTEIN FOLDING PROBLEM Understanding and predicting the three-dimensional structures