Standout Papers
Citation Impact
Citing Papers
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations
2014 StandoutNobel
Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water
2017 StandoutScienceNobel
Global analysis of protein folding using massively parallel design, synthesis, and testing
2017 StandoutScienceNobel
Atomic-Level Characterization of the Structural Dynamics of Proteins
2010 StandoutScienceNobel
Protein homology model refinement by large-scale energy optimization
2018 StandoutNobel
Accelerating molecular simulations of proteins using Bayesian inference on weak information
2015
Topological control of cytokine receptor signaling induces differential effects in hematopoiesis
2019 StandoutScienceNobel
De novo design of transmembrane β barrels
2021 StandoutScienceNobel
Sculpting conducting nanopore size and shape through de novo protein design
2024 StandoutScienceNobel
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6
2004 Standout
Molecular dynamics simulations of Leu-enkephalin in water and DMSO
1997
GROMACS: Fast, flexible, and free
2005 Standout
Ultrafast Conformational Dynamics in Cyclic Azobenzene Peptides of Increased Flexibility
2004
Modeling electrostatic effects in proteins
2006 StandoutNobel
High-resolution crystal structure of human protease-activated receptor 1
2012 StandoutNatureNobel
The twists and turns of β‐peptides
1999
Empirical force fields for biological macromolecules: Overview and issues
2004
Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model
1998
Voltage-Dependent Insertion of Alamethicin at Phospholipid/Water and Octane/Water Interfaces
2001
Vibrational circular dichroism and ab initio structure elucidation of an aromatic foldamer
2006
Force Field Bias in Protein Folding Simulations
2009
The Amber biomolecular simulation programs
2005 Standout
A new force field for simulating phosphatidylcholine bilayers
2009
Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers
2009
Structure and function of an irreversible agonist-β2 adrenoceptor complex
2011 StandoutNatureNobel
Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation
2015
A Position-Specific Distance-Dependent Statistical Potential for Protein Structure and Functional Study
2012
Structural and energetic basis of folded-protein transport by the FimD usher
2013 StandoutNatureNobel
Relaxation time prediction for a light switchable peptide by molecular dynamics
2010
Unraveling hot spots in binding interfaces: progress and challenges
2002
Solution structure of a minor and transiently formed state of a T4 lysozyme mutant
2011 StandoutNatureNobel
Conformational sampling for the impatient
2004
Design of protein switches based on an ensemble model of allostery
2015
The fundamentals of protein folding: bringing together theory and experiment
1999
Comparison of multiple Amber force fields and development of improved protein backbone parameters
2006 Standout
Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine “dipeptides” (Ace‐Ala‐Nme and Ace‐Gly‐Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
2003
The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios
2000
PASTA 2.0: an improved server for protein aggregation prediction
2014
Improved protein structure prediction using potentials from deep learning
2020 StandoutNatureNobel
TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action
2016 StandoutNatureNobel
An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer
2005
De novo design of bioactive protein switches
2019 StandoutNatureNobel
The Unfolded State of the Villin Headpiece Helical Subdomain: Computational Studies of the Role of Locally Stabilized Structure
2006
MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries
1999
Validation of all-atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble
2008
Structure and dynamics of the M3 muscarinic acetylcholine receptor
2012 StandoutNatureNobel
A surprising simplicity to protein folding
2000 StandoutNatureNobel
Energy landscape of a peptide consisting of α‐helix, 310‐helix, β‐turn, β‐hairpin, and other disordered conformations
2001
How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?
2011
Understanding protein folding via free-energy surfaces from theory and experiment
2000
Absolute comparison of simulated and experimental protein-folding dynamics
2002 Nature
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
2009 Standout
Probing Protein Fold Space with a Simplified Model
2007 StandoutNobel
Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf
2003
The GROMOS software for biomolecular simulation: GROMOS05
2005
Molecular dynamics simulations of peptides from BPTI: A closer look at amide—aromatic interactions
1996
Energy landscape of a small peptide revealed by dihedral angle principal component analysis
2004
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology
2004
Solution Conformations of Helix-Forming β-Amino Acid Homooligomers
2000
Basic conformers in ?-peptides
1999
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
2004 StandoutNobel
Ligand configurational entropy and protein binding
2007
From DARPins to LoopDARPins: Novel LoopDARPin Design Allows the Selection of Low Picomolar Binders in a Single Round of Ribosome Display
2013
Prediction of the structure of symmetrical protein assemblies
2007 StandoutNobel
Near-native structure refinement using in vacuo energy minimization
2007 StandoutNobel
An application of flexible constraints in Monte Carlo simulations of the isobaric–isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge densities in harmonic oscillators model
2004
Stereochemical Control of Hairpin Formation in β-Peptides Containing Dinipecotic Acid Reverse Turn Segments
2000
A potential model for the study of ices and amorphous water: TIP4P/Ice
2005 Standout
Efficient free energy calculations on small molecule host‐guest systems—A combined linear interaction energy/one‐step perturbation approach
2008
Random-coil behavior and the dimensions of chemically unfolded proteins
2004
Blind protein structure prediction using accelerated free-energy simulations
2016
Hydration Dynamics and Time Scales of Coupled Water−Protein Fluctuations
2007
Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems
2000
Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and validates molecular dynamics simulation
2002
Picosecond conformational transition and equilibration of a cyclic peptide
2003
Chiral Architectures from Macromolecular Building Blocks
2001
Ultrafast solvation dynamics at binding and active sites of photolyases
2010 StandoutNobel
α-Helical stabilization by side chain shielding of backbone hydrogen bonds
2002
Chiroptical Molecular Switches
2000 StandoutNobel
Theoretical Study on Side-Chain Control of the 14-Helix and the 10/12-Helix of β-Peptides
1999
Development of a simple, self-consistent polarizable model for liquid water
2002
Use of Molecular Dynamics in the Design and Structure Determination of a Photoinducible β-Hairpin
2005
Conformational analysis of (R,S)-4-amido-2,4-dimethyl-butyric acid derivatives
1999
CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes
2007
Catalytic Effects of Mutations of Distant Protein Residues in Human DNA Polymerase β: Theory and Experiment
2012 StandoutNobel
Significant Refinement of Protein Structure Models Using a Residue-Specific Force Field
2015
Catalytic Asymmetric Hydroalkoxylation of C–C Multiple Bonds
2021 StandoutNobel
Examining the secondary structures of unnatural peptides and carbohydrate-based compounds utilizing circular dichroism
2000
Roles of mutation and recombination in the evolution of protein thermodynamics
2002 StandoutNobel
NMR Structure in methanol of a β-hexapeptide with a disulfide clamp
2000
β-Peptides: From Structure to Function
2001 Standout
Foldamer-Based Molecular Recognition
2000
Folding of a donor–acceptor polyrotaxane by using noncovalent bonding interactions
2008 StandoutNobel
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase
2008 StandoutNobel
Hydrazino Peptides as Foldamers: An Extension of the β-Peptide Concept
2000
Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model
2005
Solvent dramatically affects protein structure refinement
2008 StandoutNobel
De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures
2017 StandoutNobel
A general purpose model for the condensed phases of water: TIP4P/2005
2005 Standout
Absolute entropies from molecular dynamics simulation trajectories
2000
Molecular dynamics and protein function
2005
Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice
2004
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
2010 Standout
Conformational Dynamics of Trialanine in Water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS Force Fields to NMR and Infrared Experiments
2003
Reversible Photocontrol of Biological Systems by the Incorporation of Molecular Photoswitches
2013 StandoutNobel
A Field Guide to Foldamers
2001 Standout
Context and Force Field Dependence of the Loss of Protein Backbone Entropy upon Folding Using Realistic Denatured and Native State Ensembles
2012
Computer simulations of protein functions: Searching for the molecular origin of the replication fidelity of DNA polymerases
2005 StandoutNobel
Fast Kinetics and Mechanisms in Protein Folding
2000
Progress in Modeling of Protein Structures and Interactions
2005 StandoutScienceNobel
Theoretical Studies of β-Peptide Models
1998
Reversible Optical Transcription of Supramolecular Chirality into Molecular Chirality
2004 StandoutScienceNobel
An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers
2009
How Fast-Folding Proteins Fold
2011 Science
Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F 0 -ATPase
2012 StandoutNobel
Preparation of N‐Fmoc‐Protected β2‐ and β3‐Amino Acids and their use as building blocks for the solid‐phase synthesis of β‐peptides
1998
Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model
2006
Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase β's closing
2004
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
1999
Improved treatment of cyclic ?-amino acids and successful prediction of ?-peptide secondary structure using a modified force field: AMBER*C
2000
Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural, and dielectric properties of liquid water
1998
Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins
2008
Brute-Force Molecular Dynamics Simulations of Villin Headpiece: Comparison with NMR Parameters
2003
Quantum Mechanical Continuum Solvation Models
2005 Standout
Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins
2003
α-Helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy
2005
Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin
2016
Molecular dynamics simulation of hen egg white lysozyme: A test of the GROMOS96 force field against nuclear magnetic resonance data
2000
General Framework for Studying the Dynamics of Folded and Nonfolded Proteins by NMR Relaxation Spectroscopy and MD Simulation
2002
United-Atom Acyl Chains for CHARMM Phospholipids
2008
Computational Design of Stable and Soluble Biocatalysts
2018
β2‐ and β3‐Peptides with Proteinaceous Side Chains: Synthesis and solution structures of constitutional isomers, a novel helical secondary structure and the influence of solvation and hydrophobic interactions on folding
1998
Evaluation of Configurational Entropy Methods from Peptide Folding−Unfolding Simulation
2007
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
2004 Standout
Entropy Localization in Proteins
2010
Influence of Artificial Periodicity and Ionic Strength in Molecular Dynamics Simulations of Charged Biomolecules Employing Lattice-Sum Methods
2003
On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes
2010 StandoutNobel
A simple physical model for binding energy hot spots in protein–protein complexes
2002 StandoutNobel
Works of Xavier Daura being referenced
AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides
2007
Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme
2004
On the sensitivity of MD trajectories to changes in water-protein interaction parameters: The potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field
1996
Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations
2001
Biomolecular Modeling: Goals, Problems, Perspectives
2006
Reversible peptide folding in solution by molecular dynamics simulation 1 1Edited by R. Huber
1998
A novel approach for designing simple point charge models for liquid water with three interaction sites
2003
β‐Hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution
2004
Unfolded state of peptides
2002
Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds
2001
Folding-unfolding thermodynamics of a ?-heptapeptide from equilibrium simulations
1999
Factor Xa: Simulation studies with an eye to inhibitor design
2000
Assessing equilibration and convergence in biomolecular simulations
2002
Molecular dynamics simulations of peptides containing an unnatural amino acid: Dimerization, folding, and protein binding
2003
Configurational entropy elucidates the role of salt‐bridge networks in protein thermostability
2007
The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State
2001
Circular dichroism spectra of β-peptides: sensitivity to molecular structure and effects of motional averaging
2003
Derivation of an improved simple point charge model for liquid water: SPC/A and SPC/L
2002
Validation of molecular simulation by comparison with experiment: Rotational reorientation of tryptophan in water
1999
Τhe β-Peptide Hairpin in Solution: Conformational Study of a β-Hexapeptide in Methanol by NMR Spectroscopy and MD Simulation
2001
Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior
2001
Computation of Free Energy
2002
Free Energies of Transfer of Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions
1996
Peptide folding simulations: no solvent required?
1999
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
2001
Peptides of Aminoxy Acids: A Molecular Dynamics Simulation Study of Conformational Equilibria under Various Conditions
2000
Oligonucleotide Analogues with a Nucleobase-Including Backbone, Part 7, Molecular Dynamics Simulation of a DNA Duplex Containing a 2′-Deoxyadenosine 8-(Hydroxymethyl)-Derived Nucleotide
2001
Peptidfaltung: Wenn die Simulation das Experiment erreicht
1999
-Peptides with Different Secondary-Structure Preferences: How Different Are Their Conformational Spaces?
2002
Structure and Conformation ofβ-Oligopeptide Derivatives with Simple Proteinogenic Side Chains: Circular Dichroism and Molecular Dynamics Investigations
2000
Can One Derive the Conformational Preference of a β-Peptide from Its CD Spectrum?
2002
A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization
2001
On the transferability of the SPC/L water model to biomolecular simulation
2004
Peptide Folding: When Simulation Meets Experiment
1999 Standout
Studying the Stability of a Helical β‐Heptapeptide by Molecular Dynamics Simulations
1997
Parametrization of aliphatic CHn united atoms of GROMOS96 force field
1998
Molecular Dynamics Simulation of Biomolecular Systems
2001