Standout Papers
Citation Impact
Citing Papers
Ion motions in molecular dynamics simulations on DNA
2004
High-Resolution Crystal Structure of an Engineered Human β 2 -Adrenergic G Protein–Coupled Receptor
2007 StandoutScienceNobel
Atomic-Level Characterization of the Structural Dynamics of Proteins
2010 StandoutScienceNobel
GPCR Engineering Yields High-Resolution Structural Insights into β 2 -Adrenergic Receptor Function
2007 StandoutScienceNobel
NMR structure reveals intramolecular regulation mechanism for pheromone binding and release
2001 StandoutNobel
Reaction coordinates and rates from transition paths
2005
Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction
2010 StandoutScienceNobel
Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments
2009
Structure of the signal recognition particle interacting with the elongation-arrested ribosome
2004 StandoutNatureNobel
Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints
2003
Theoretical methods for the simulation of nucleic acids
2003
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
2010 Standout
Molecular dynamics simulations and their application to four-stranded DNA
2007
Force Fields for Protein Simulations
2003
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy
2003 StandoutNobel
Cooperativity in noncovalent interactions of biologically relevant molecules
2009
Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation
2002 Standout
Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
2000
NMR structure of the mouse prion protein domain PrP(121–231)
1996 StandoutNatureNobel
Molecular Dynamics and Continuum Solvent Studies of the Stability of PolyG-PolyC and PolyA-PolyT DNA Duplexes in Solution
1998
Energy functions for protein design
1999
Computer simulation studies of the fidelity of DNA polymerases
2003 StandoutNobel
Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex
2004
Protein NMR Structure Determination with Automated NOE Assignment Using the New Software CANDID and the Torsion Angle Dynamics Algorithm DYANA
2002 StandoutNobel
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
2007 Standout
Functional conformations of the L11–ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations
2006 StandoutNobel
Crystal structure of the human β2 adrenergic G-protein-coupled receptor
2007 StandoutNatureNobel
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch
2009
High-resolution crystal structure of human protease-activated receptor 1
2012 StandoutNatureNobel
Empirical force fields for biological macromolecules: Overview and issues
2004
Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors
2010
Continuum Solvent Studies of the Stability of RNA Hairpin Loops and Helices
1998
Refinement of protein structures in explicit solvent
2003
Conformational analysis of protein and nucleic acid fragments with the new grid search algorithm FOUND
1998 StandoutNobel
CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields
2009 Standout
Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme
2006
Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E
2003
Protein WISDOM: A Workbench for <em>In silico</em> <em>De novo</em> Design of BioMolecules
2013
What recent ribosome structures have revealed about the mechanism of translation
2009 StandoutNatureNobel
Simultaneous determination of protein structure and dynamics
2005
Principles for designing ideal protein structures
2012 StandoutNatureNobel
Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamic Analysis of the Substates
2003
Structure and function of an irreversible agonist-β2 adrenoceptor complex
2011 StandoutNatureNobel
Molecular dynamics simulations of RNA: An in silico single molecule approach
2006
Modeling of loops in protein structures
2000 Standout
Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-Minor Motif and Nominally Unpaired Bases
2005
The coming of age of de novo protein design
2016 StandoutNatureNobel
Water conduction through the hydrophobic channel of a carbon nanotube
2001 StandoutNature
Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites
2021 StandoutNobel
Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge
2004
Predicting protein structures with a multiplayer online game
2010 StandoutNatureNobel
Symmetric K+ and Mg2+ Ion-binding Sites in the 5S rRNA Loop E Inferred from Molecular Dynamics Simulations
2003
RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics
2006
Automated combined assignment of NOESY spectra and three-dimensional protein structure determination
1997 StandoutNobel
An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes
2003 StandoutNobel
Development and testing of a general amber force field
2004 Standout
The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios
2000
Improved protein structure prediction using potentials from deep learning
2020 StandoutNatureNobel
The Disordered Mobile Loop of GroES Folds into a Defined β-Hairpin upon Binding GroEL
2001
NMR analysis of a 900K GroEL–GroES complex
2002 StandoutNatureNobel
A short guide for molecular dynamics simulations of RNA systems
2008
A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex.
1999
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM
2009 StandoutNobel
Role of Hydrogen Bonds in Protein-DNA Recognition: A Comparison of Generalized Born and Finite Difference Poisson-Boltzmann Solvation Treatments
1998
Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
2004 Standout
Protein‐based virtual screening of chemical databases. II. Are homology models of g‐protein coupled receptors suitable targets?
2002
Dynamic Coupling between the SH2 and SH3 Domains of c-Src and Hck Underlies Their Inactivation by C-Terminal Tyrosine Phosphorylation
2001
Structure and dynamics of the M3 muscarinic acetylcholine receptor
2012 StandoutNatureNobel
Molecular Simulation Studies of Monovalent Counterion-Mediated Interactions in a Model RNA Kissing Loop
2009
Structural Basis for the Autoinhibition of c-Abl Tyrosine Kinase
2003 Standout
A surprising simplicity to protein folding
2000 StandoutNatureNobel
An improved protein decoy set for testing energy functions for protein structure prediction
2003 StandoutNobel
Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics
2007
Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems
1998
Prion (PrPSc)-specific epitope defined by a monoclonal antibody
1997 StandoutNatureNobel
Torsion angle dynamics for NMR structure calculation with the new program Dyana
1997 StandoutNobel
De novo protein design by deep network hallucination
2021 StandoutNatureNobel
A Conserved Protonation-Induced Switch can Trigger “Ionic-Lock” Formation in Adrenergic Receptors
2010
Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps
2005
Structural Dynamics of Precursor and Product of the RNA Enzyme from the Hepatitis Delta Virus as Revealed by Molecular Dynamics Simulations
2005
Structure and IR Spectrum of Phenylalanyl–Glycyl–Glycine Tripetide in the Gas‐Phase: IR/UV Experiments, Ab Initio Quantum Chemical Calculations, and Molecular Dynamic Simulations
2005
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA
2007
NMR structures of three single-residue variants of the human prion protein
2000 StandoutNobel
Treatment of the outlying charge in continuum solvation models
1996
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
1996 Standout
Optimization of solute cavities and van der Waals parameters in ab initio MST‐SCRF calculations of neutral molecules
1994
The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution
2000 StandoutScienceNobel
Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
2007
Incorporation of reaction field effects into density functional calculations for molecules of arbitrary shape in solution
1994
Free Energy Perturbation Study of Octanol/Water Partition Coefficients: Comparison with Continuum GB/SA Calculations
1999
Excited states and solvatochromic shifts within a nonequilibrium solvation approach: A new formulation of the integral equation formalism method at the self-consistent field, configuration interaction, and multiconfiguration self-consistent field level
1998
Escaping free-energy minima
2002 Standout
Extension of MST/SCRF method to organic solvents:Ab initio and semiempirical parametrization for neutral solutes in CCl4
1996
Toward an effective and reliable representation of solvent effects in the study of biochemical systems
1999
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields
2009
Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?
2007
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations
2006
Remarks on the use of the apparent surface charges (ASC) methods in solvation problems: Iterative versus matrix‐inversion procedures and the renormalization of the apparent charges
1995
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
2000
Experimental Determination of the Absolute Enantioselectivity of an Antibody-Catalyzed Diels−Alder Reaction and Theoretical Explorations of the Origins of Stereoselectivity
2003
Selective Targeting of Integrin αvβ8 by a Highly Active Cyclic Peptide
2019
Energetics of charge transfer reactions in solvents of dipolar and higher order multipolar character. II. Results
1996
Solvation effects in SINDO1: Application to organic molecules
1997
Toward High-Resolution de Novo Structure Prediction for Small Proteins
2005 StandoutScienceNobel
Adapting free energy perturbation simulations for large macrocyclic ligands: how to dissect contributions from direct binding and free ligand flexibility
2020
Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution
1998 Science
Calculation of UV/Vis Spectra in Solution
1996
Theoretical Investigation of the Binding Free Energies and Key Substrate-Recognition Components of the Replication Fidelity of Human DNA Polymerase β
2002 StandoutNobel
Calculation of solvatochromic shifts using MC-SCF theory. The n—π* transition of acetone
1993
Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry
1996
Performance of the AMBER94, MMFF94, and OPLS-AA Force Fields for Modeling Organic Liquids
1996
Dynamics of B-DNA on the Microsecond Time Scale
2007
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
1995 Standout
Noncovalent Interactions: A Challenge for Experiment and Theory
1999 Standout
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
1999 Standout
Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins
1995
Computer Simulation of the Chemical Catalysis of DNA Polymerases: Discriminating between Alternative Nucleotide Insertion Mechanisms for T7 DNA Polymerase
2003 StandoutNobel
VB resonance theory in solution. I. Multistate formulation
1995
Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor
2013 StandoutNobel
Nanosecond Molecular Dynamics Simulations of Parallel and Antiparallel Guanine Quadruplex DNA Molecules
1999
Evidence for the Conformation of the Pathologic Isoform of the Prion Protein Enciphering and Propagating Prion Diversity
1996 StandoutScienceNobel
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
2000 Standout
Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
2008 Standout
Prion Diseases and the BSE Crisis
1997 StandoutScienceNobel
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
2003 StandoutScienceNobel
Automatic parameterization of force field by systematic search and genetic algorithms
2001
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
1996 Standout
Macromolecular Modeling with Rosetta
2008 StandoutNobel
A consistent and accurateab initioparametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
2010 Standout
Computer simulations of protein functions: Searching for the molecular origin of the replication fidelity of DNA polymerases
2005 StandoutNobel
NMR solution structure of the human prion protein
2000 StandoutNobel
Progress in Modeling of Protein Structures and Interactions
2005 StandoutScienceNobel
What Controls Partitioning of the Nucleic Acid Bases between Chloroform and Water?
1997
Protein Structure Prediction and Structural Genomics
2001 StandoutScienceNobel
Transfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data
2007 StandoutNobel
Role of group-conserved residues in the helical core of β 2 -adrenergic receptor
2007
Solvent effects on electronic spectra studied by multiconfigurational perturbation theory
1997
Langevin Dipoles Model for ab Initio Calculations of Chemical Processes in Solution: Parametrization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution
1997 StandoutNobel
Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), andab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results
1997
Intrinsic and Environmental Effects in the Structure and Magnetic Properties of Glycine Radical in Aqueous Solution
1997
Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field
1998
Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1
2000
Anisotropy of the Induced Current Density (ACID), a General Method To Quantify and Visualize Electronic Delocalization
2005 Standout
Electrostatic interactions in macromolecules
1994
Effect of solvent fluctuation on the electronic transitions of formaldehyde in aqueous solution
1999
Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets
2003
Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: NonempiricalAb InitioCalculations
1999
Including Side Chain Flexibility in Continuum Electrostatic Calculations of Protein Titration
1996
Three-Dimensional Models for β-Adrenergic Receptor Complexes with Agonists and Antagonists
2003
Uracil Dimer: Potential Energy and Free Energy Surfaces. Ab Initio beyond Hartree−Fock and Empirical Potential Studies
1998
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
1998
The Protein Folding Problem
2008
Theoretical evaluation of medium effects on absorption maxima of molecular solutes. I. Formulation of a new method based on the self-consistent reaction field theory
1997
2.1 and 1.8 Å Average Cα RMSD Structure Predictions on Two Small Proteins, HP-36 and S15
2001 StandoutNobel
NMR structure of the calreticulin P-domain
2001 StandoutNobel
Solution Structure of Syrian Hamster Prion Protein rPrP(90−231)
1999 Nobel
The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules
1996
Calculation of Alkane to Water Solvation Free Energies Using Continuum Solvent Models
1996
A smooth particle mesh Ewald method
1995 Standout
Works of Thomas Fox being referenced
The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: How well is the x‐ray structure “maintained”?
1996
Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the α → β Anomerization of Glucose
1998
On the cavity model for solvent shifts of excited states — a critical appraisal
1992
The calculation of solvatochromic shifts: the n-π* transition of acetone
1992
Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization
2018
Electrostatic solvent effects on the electronic structure of ground and excited states of molecules: Applications of a cavity model based upon a finite element method
1993
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
1995 Standout
A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions
1997
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197
1996
Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins
1995
Application of the RESP Methodology in the Parametrization of Organic Solvents
1998