Citation Impact
Citing Papers
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations
2014 StandoutNobel
Thermodynamic prediction of protein neutrality
2005 StandoutNobel
Atomic-Level Characterization of the Structural Dynamics of Proteins
2010 StandoutScienceNobel
Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy
2017 Science
Protein homology model refinement by large-scale energy optimization
2018 StandoutNobel
Single Reconstituted Neuronal SNARE Complexes Zipper in Three Distinct Stages
2012 StandoutScienceNobel
SNARE Proteins: One to Fuse and Three to Keep the Nascent Fusion Pore Open
2012 StandoutScienceNobel
Origins of coevolution between residues distant in protein 3D structures
2017 StandoutNobel
Reaction coordinates and rates from transition paths
2005
Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
2011 StandoutNobel
Accurate computational design of multipass transmembrane proteins
2018 StandoutScienceNobel
Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase
1992 StandoutNobel
The protein folding ‘speed limit’
2004
Principles of protein folding — A perspective from simple exact models
1995
New Monte Carlo algorithms for protein folding
1999
Sub-microsecond Protein Folding
2006
Enhanced Toxicity and Cellular Binding of a Modified Amyloid β Peptide with a Methionine to Valine Substitution
2004
Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution
2012 StandoutNobel
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers
2012 StandoutNobel
The Alzheimer's Peptide Aβ Adopts a Collapsed Coil Structure in Water
2000
Capturing the essence of folding and functions of biomolecules using coarse-grained models
2011
Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins
2011 Nature
Genetically programmed chiral organoborane synthesis
2017 StandoutNatureNobel
Improved sampling methods for molecular simulation
2007
High-resolution structure prediction and the crystallographic phase problem
2007 StandoutNatureNobel
Mean-field minimization methods for biological macromolecules
1996
Polypeptide chain collapse and protein folding
2012
Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations
2011
Peptide‐Based Inhibitors of Amyloid Assembly
2006
Influence of protein structure databases on the predictive power of statistical pair potentials
1998
Dynamics of biochemical and biophysical reactions: insight from computer simulations
2001 StandoutNobel
Dimeric interactions and complex formation using direct coevolutionary couplings
2015
Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation
2011 StandoutNatureNobel
Template-directed synthesis of a genetic polymer in a model protocell
2008 StandoutNatureNobel
Elucidation of Primary Structure Elements Controlling Early Amyloid β-Protein Oligomerization
2003
Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles
2013
Computational design of a synthetic PD-1 agonist
2021 StandoutNobel
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
2004 StandoutNobel
Comments on a paper by Straub, Borkovec, and Berne
1987
Near-native structure refinement using in vacuo energy minimization
2007 StandoutNobel
Nonequilibrium solvation effects on reaction rates for model SN2 reactions in water
1989
Dynamical Contributions to Enzyme Catalysis: Critical Tests of A Popular Hypothesis
2006 StandoutNobel
Quantum energy flow during molecular isomerization
1997
Molecular-dynamics simulation for a model nonadiabatic proton transfer reaction in solution
1991
Computational method to reduce the search space for directed protein evolution
2001 StandoutNobel
Ultrafast Hydration Dynamics in Melittin Folding and Aggregation: Helix Formation and Tetramer Self-Assembly
2005
Dynamics of an Enzymatic Substitution Reaction in Haloalkane Dehalogenase
2004
Activated barrier crossing for many degrees of freedom: Corrections to the low friction Kramers result
1987
Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization
2010 StandoutNobel
Molecular dynamics with electronic transitions
1990 Standout
A new paradigm for electrostatic catalysis of radical reactions in vitamin B 12 enzymes
2007 StandoutNobel
Effect of time-delayed friction on the escape from a metastable well
1988
Escape from a metastable state
1986
Mean first passage time and the lifetime of a metastable state
1987
Ultrafast solvation dynamics at binding and active sites of photolyases
2010 StandoutNobel
Transition rates of a non-Markovian Brownian particle in a double well potential
1988
Hopping and the Stokes–Einstein relation breakdown in simple glass formers
2014 StandoutNobel
Quantum Mechanics of a Macroscopic Variable: The Phase Difference of a Josephson Junction
1988 StandoutScienceNobel
Femtosecond dynamics of the DNA intercalator ethidium and electron transfer with mononucleotides in water
1999 StandoutNobel
Observation of the kramers turnover region in the isomerism of trans-stilbene in fluid ethane
1985
Quantum annealing by the path-integral Monte Carlo method: The two-dimensional random Ising model
2002
Tinker 8: Software Tools for Molecular Design
2018
Copper Homeostasis and Neurodegenerative Disorders (Alzheimer's, Prion, and Parkinson's Diseases and Amyotrophic Lateral Sclerosis)
2006 Standout
A position dependent friction model for solution reactions in the high friction regime: Proton transfer in triosephosphate isomerase (TIM)
1996
Quantum Brownian motion: The functional integral approach
1988
Rate constants for ion pair formation and dissociation in water
1986
Roles of mutation and recombination in the evolution of protein thermodynamics
2002 StandoutNobel
Promoting Modes and Demoting Modes in Enzyme-Catalyzed Proton Transfer Reactions: A Study of Models and Realistic Systems
2002
Simulation of activation free energies in molecular systems
1996
High thermodynamic stability of parametrically designed helical bundles
2014 StandoutScienceNobel
Dimensional study of the caging order parameter at the glass transition
2012 StandoutNobel
Femtosecond Activation of Reactions and the Concept of Nonergodic Molecules
1998 StandoutScienceNobel
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase
2008 StandoutNobel
Native protein sequences are close to optimal for their structures
2000 StandoutNobel
Theory of dynamic barriers, activated hopping, and the glass transition in polymer melts
2004
Direct observation of kinetic traps associated with structural transformations leading to multiple pathways of S-layer assembly
2012 StandoutNobel
WATER MEDIATION IN PROTEIN FOLDING AND MOLECULAR RECOGNITION
2006
Characterization of Chemical Exchange between Soluble and Aggregated States of β-Amyloid by Solution-State NMR upon Variation of Salt Conditions
2005
Solvent dramatically affects protein structure refinement
2008 StandoutNobel
Defining and detecting quantum speedup
2014 StandoutScienceNobel
De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures
2017 StandoutNobel
Viscosity Dependence of the Folding Rates of Proteins
1997
Chemical Dynamics in Solution
1990
Reaction-rate theory: fifty years after Kramers
1990 Standout
Coupling the folding of homologous proteins
1998
Progress in Modeling of Protein Structures and Interactions
2005 StandoutScienceNobel
Molecular model for aqueous ferrous–ferric electron transfer
1988
Global Optimization of Clusters, Crystals, and Biomolecules
1999 Science
Chemical Reactions and Solvation at Liquid Interfaces: A Microscopic Perspective
1996
Theories of intramolecular vibrational energy transfer
1991
Bistability and Colored Noise in Nonequilibrium Systems: Theory versus Precise Numerics
1988
Electrostatic Basis for Enzyme Catalysis
2006 StandoutNobel
Fluctuating Enzymes: Lessons from Single-Molecule Studies
2005
Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F 0 -ATPase
2012 StandoutNobel
New directions in single-molecule imaging and analysis
2007 StandoutNobel
Femtosecond solvation dynamics of water
1994 Nature
Theory of activated rate processes for arbitrary frequency dependent friction: Solution of the turnover problem
1989
Dielectric Relaxation and Solvation Dynamics of Water in Complex Chemical and Biological Systems
2000
Computer simulations of enzyme catalysis: Finding out what has been optimized by evolution
1998 StandoutNobel
Effect of β-sheet propensity on peptide aggregation
2009
Direct characterization of amyloidogenic oligomers by single-molecule fluorescence
2008
Enzyme millisecond conformational dynamics do not catalyze the chemical step
2009 StandoutNobel
Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
1993 StandoutNobel
Quantum Mechanical Continuum Solvation Models
2005 Standout
Inhibitors of Amyloid Toxicity Based on β-sheet Packing of Aβ40 and Aβ42
2006
Entropic barriers, activated hopping, and the glass transition in colloidal suspensions
2003
Variational transition-state theory for reaction rates in dissipative systems
1990
Numerical integration of stochastic differential equations
1988
Solvent dielectric effects on isomerization dynamics: Investigation of the photoisomerization of 4,4′-dimethoxystilbene and t-stilbene in n-alkyl nitriles
1989
Kinetics of protein folding: Nucleation mechanism, time scales, and pathways
1995
Escape from a Metastable Well: The Kramers Turnover Problem
1988
A simple physical model for binding energy hot spots in protein–protein complexes
2002 StandoutNobel
Mechanism of Unassisted Ion Transport across Membrane Bilayers
1996
Limited internal friction in the rate-limiting step of a two-state protein folding reaction
1998 StandoutNobel
Quantum Mechanics/Molecular Mechanics Studies of Triosephosphate Isomerase-Catalyzed Reactions: Effect of Geometry and Tunneling on Proton-Transfer Rate Constants
2002
Unified approach to the quantum-Kramers reaction rate
1988
Works of John E. Straub being referenced
Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide
1996
Probing the Initial Stage of Aggregation of the Aβ10-35-protein: Assessing the Propensity for Peptide Dimerization
2004
Structural and dynamical analysis of the hydration of the Alzheimer's β‐amyloid peptide
2002
The interpretation of site-directed mutagenesis experiments by linear free energy relations
1990
Theoretical probes of conformational fluctuations in S‐peptide and RNase A/3′–UMP enzyme product complex
1993
Principles governing oligomer formation in amyloidogenic peptides
2010
Simulation Study of the Structure and Dynamics of the Alzheimer’s Amyloid Peptide Congener in Solution
2001
A Study of Vibrational Relaxation of B-State Carbon Monoxide in the Heme Pocket of Photolyzed Carboxymyoglobin
1999
Novel methods of sampling phase space in the simulation of biological systems
1997
Energy equipartitioning in the classical time-dependent Hartree approximation
1991
Non-Markovian activated rate processes: Comparison of current theories with numerical simulation data
1986
Calculation of dynamic friction on intramolecular degrees of freedom
1987
On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters
1997
Dynamics in Rugged Energy Landscapes with Applications to the S-Peptide and Ribonuclease A
1994
The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature
1997
The influence of intramolecular vibrational relaxation on the pressure dependence of unimolecular rate constants
1986
Molecular dynamics simulation of NO recombination to myoglobin mutants.
1993
Simulation study of the collapse of linear and ring homopolymers
1995
Folding model proteins using kinetic and thermodynamic annealing of the classical density distribution
1995
A statistical theory for the effect of nonadiabatic transitions on activated processes
1987
Dynamic friction on rigid and flexible bonds
1990
Time scales and pathways for kinetic energy relaxation in solvated proteins: Application to carbonmonoxy myoglobin
2000
Global energy minimum searches using an approximate solution of the imaginary time Schroedinger equation
1993
Classical and modern methods in reaction rate theory
1988
Long Time Dynamic Simulations: Exploring the Folding Pathways of an Alzheimer's Amyloid Aβ-Peptide
2002
Molecular dynamics study of an isomerizing diatomic in a Lennard-Jones fluid
1988
Aqueous urea solution destabilizes Aβ16–22oligomers
2004
A Molecular Switch in Amyloid Assembly: Met35and Amyloid β-Protein Oligomerization
2003
Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock–lock mechanism
2006
Shortcomings of current theories of non-Markovian activated rate processes
1985
Approximate solution of the classical Liouville equation using Gaussian phase packet dynamics: Application to enhanced equilibrium averaging and global optimization
1993
Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: Comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations
1999
Energy diffusion in many-dimensional Markovian systems: The consequences of competition between inter- and intramolecular vibrational energy transfer
1986
Finding the needle in the haystack: Algorithms for conformational optimization
1996
On determining reaction kinetics by molecular dynamics using absorbing barriers
1985
Simulated annealing using the classical density distribution
1994
Exploring the energy landscape in proteins.
1993
Transmembrane Structures of Amyloid Precursor Protein Dimer Predicted by Replica-Exchange Molecular Dynamics Simulations
2009
A rapid method for determining rate constants by molecular dynamics
1985
Numerical simulation of rate constants for a two degree of freedom system in the weak collision limit
1987
Diversity of Solvent Dependent Energy Transfer Pathways in Heme Proteins
2008