Citation Impact
Citing Papers
Proton Binding to Proteins: p K a Calculations with Explicit and Implicit Solvent Models
2004
Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation
2014 StandoutScienceNobel
Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy
2012 StandoutScienceNobel
Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage
2016 StandoutScienceNobel
High-Resolution Crystal Structure of an Engineered Human β 2 -Adrenergic G Protein–Coupled Receptor
2007 StandoutScienceNobel
Global analysis of protein folding using massively parallel design, synthesis, and testing
2017 StandoutScienceNobel
Comprehensive computational design of ordered peptide macrocycles
2017 StandoutScienceNobel
Accurate computational design of multipass transmembrane proteins
2018 StandoutScienceNobel
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
Structural Mechanisms for Domain Movements in Proteins
1994
Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
2000
Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
1997
Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution
2003
NMR structure of the mouse prion protein domain PrP(121–231)
1996 StandoutNatureNobel
Faster superoxide dismutase mutants designed by enhancing electrostatic guidance
1992 Nature
Atomic model of the type III secretion system needle
2012 StandoutNatureNobel
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
2003
X-Ray Structure of Acid-Sensing Ion Channel 1–Snake Toxin Complex Reveals Open State of a Na+-Selective Channel
2014 StandoutNobel
GB/SA water model for the Merck molecular force field (MMFF)
2000
Modeling electrostatic effects in proteins
2006 StandoutNobel
Improving implicit solvent simulations: a Poisson-centric view
2005
Inference of Macromolecular Assemblies from Crystalline State
2007 Standout
Structural Determinants of Proton Blockage in Aquaporins
2004
Acetylcholinesterase: electrostatic steering increases the rate of ligand binding
1993
Future directions for combining molecular and continuum models in protein simulations
1998
pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis.
1995
A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein–water interface as a determinant of pKavalues
2008
Structure of the Type VI Secretion System Contractile Sheath
2015 StandoutNobel
H++: a server for estimating pKas and adding missing hydrogens to macromolecules
2005
Instability and decay of the primary structure of DNA
1993 StandoutNatureNobel
Empirical force fields for biological macromolecules: Overview and issues
2004
Electrostatic fields in antibodies and antibody/antigen complexes
1992
Irritant-evoked activation and calcium modulation of the TRPA1 receptor
2020 StandoutNatureNobel
Salt effects on nucleic acids
1995
Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin
1999
Multiple‐site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins
1993
The Amber biomolecular simulation programs
2005 Standout
Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins
1994
Improving macromolecular electrostatics calculations
1999
A cryo-electron microscopic study of ribosome-bound termination factor RF2
2003 StandoutNatureNobel
Theory of electrostatic interactions in macromolecules
1995
How Optimal Are the Binding Energetics of Barnase and Barstar?
2004
Stabilization of Internal Charges in a Protein: Water Penetration or Conformational Change?
2004
UCSF Chimera—A visualization system for exploratory research and analysis
2004 Standout
A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells
2014 StandoutNobel
High-resolution structure prediction and the crystallographic phase problem
2007 StandoutNatureNobel
Structures of Human Exonuclease 1 DNA Complexes Suggest a Unified Mechanism for Nuclease Family
2011 StandoutNobel
Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials
2003
A Cell-Penetrating Scorpion Toxin Enables Mode-Specific Modulation of TRPA1 and Pain
2019 StandoutNobel
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
2003
Type IV Pilus Structure by Cryo-Electron Microscopy and Crystallography: Implications for Pilus Assembly and Functions
2006
A mechanism for rotamase catalysis by the FK506 binding protein (FKBP)
1993
Implicit solvent models
1999
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
2004 Standout
Treatment of electrostatic effects in proteins: Multigrid‐based newton iterative method for solution of the full nonlinear poisson–boltzmann equation
1994
Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme
1994
Experimental pKa Values of Buried Residues: Analysis with Continuum Methods and Role of Water Penetration
2002
Accelerated Poisson–Boltzmann calculations for static and dynamic systems
2002
Structural snapshots of TRPV1 reveal mechanism of polymodal functionality
2021 StandoutNobel
Structure of the DNA Repair and Replication Endonuclease and Exonuclease FEN-1
1998
Electrostatic effects in macromolecules: fundamental concepts and practical modeling
1998 StandoutNobel
Treatment of electrostatic effects in macromolecular modeling
1989
Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
2001
Structure of the zinc-binding domain of an essential component of the hepatitis C virus replicase
2005 StandoutNatureNobel
Conserved XPB Core Structure and Motifs for DNA Unwinding: Implications for Pathway Selection of Transcription or Excision Repair
2006
Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study
1999
Likelihood-enhanced fast translation functions
2005 Standout
Electrostatic Contributions to the Binding Free Energy of the λcI Repressor to DNA
1998
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
2007 Standout
Explicit solvent models in protein pKa calculations
1996
Electrostatic aspects of protein–protein interactions
2000
X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity
2002 StandoutNatureNobel
High Apparent Dielectric Constant Inside a Protein Reflects Structural Reorganization Coupled to the Ionization of an Internal Asp
2006
Does NMR Mean “Not for Molecular Replacement”? Using NMR-Based Search Models to Solve Protein Crystal Structures
2000
Point charge distributions and electrostatic steering in enzyme/substrate encounter: Brownian dynamics of modified copper/zinc superoxide dismutases
1990
Electrostatic Contributions to T4 Lysozyme Stability: Solvent-Exposed Charges versus Semi-Buried Salt Bridges
2002
Crystallographic Analysis of the Recognition of a Nuclear Localization Signal by the Nuclear Import Factor Karyopherin α
1998 StandoutNobel
Prediction of functionally important residues based solely on the computed energetics of protein structure 1 1Edited by B. Honig
2001
Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry
1999
Do salt bridges stabilize proteins? A continuum electrostatic analysis
1994
Cryo-EM structure of a type IV secretion system
2022 StandoutNatureNobel
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
2009 Standout
Salt effects on polyelectrolyte–ligand binding: Comparison of Poisson–Boltzmann, and limiting law/counterion binding models
1995
Benchmarking pKa prediction
2006
Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane
2020
Packaging of Proteases and Proteoglycans in the Granules of Mast Cells and Other Hematopoietic Cells
1995
A view of thermodynamics of hydration emerging from continuum studies
1994
Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves
1993
Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results
1996
The hydration and solvent polarization effects of nucleotide bases
1994
Poisson–Boltzmann Methods for Biomolecular Electrostatics
2004
Accurate design of megadalton-scale two-component icosahedral protein complexes
2016 StandoutScienceNobel
Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations
1997
A Smooth Solvation Potential Based on the Conductor-Like Screening Model
1999
Dielectric solvation dynamics of molecules of arbitrary shape and charge distribution
1998
Implicit solvation based on generalized Born theory in different dielectric environments
2003
Generalized Born Models of Macromolecular Solvation Effects
2000
A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields
1999
Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex
2013 StandoutScienceNobel
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples
2000
Fast summation boundary element method for calculating solvation free energies of macromolecules
1998
Analytical first and second energy derivatives of the generalized conductorlike screening model for free energy of solvation
1995
Multigrid solution of the Poisson—Boltzmann equation
1993
An effective fragment method for modeling solvent effects in quantum mechanical calculations
1996
Incorporation of reaction field effects into density functional calculations for molecules of arbitrary shape in solution
1994
Electrostatics and dynamics of proteins
2003
[1] Electrostatic effects in protein folding, stability, and function
1991
Development and parametrization of continuum solvent models. II. A unified approach to the solvation problem
1996
A fast and Space-efficient boundary element method for computing electrostatic and hydration effects in large molecules
1996
A dielectric continuum molecular dynamics method
2001
Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems
2000
Incorporating solvation effects into density functional theory: Calculation of absolute acidities
1997
The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations
1991
Prediction of Aqueous Solvation Free Energies from Properties of Solute Molecular Surface Electrostatic Potentials
1999
Calculation of HyHel10-lysozyme binding free energy changes: Effect of ten point mutations
1998
Modification of the Generalized Born Model Suitable for Macromolecules
2000
Ab initio study of ionic solutions by a polarizable continuum dielectric model
1998 Standout
Determination of the Stable Microstates of a Peptide from NOE Distance Constraints and Optimization of Atomic Solvation Parameters
1998
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems
2000
Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors
2013 StandoutScienceNobel
A simple yet accurate boundary element method for continuum dielectric calculations
1995
pKa Shifts in Small Molecules and HIV Protease: Electrostatics and Conformation
1998
Theoretical chemistry in solution. Some results and perspectives of the continuum methods and in particular of the polarizable continuum model
1991
Calculation of the dielectric permittivity profile for a nonuniform system: Application to a lipid bilayer simulation
2003
Comparison of Continuum and Explicit Models of Solvation: Potentials of Mean Force for Alanine Dipeptide
1996
Electrostatics
1992
Calculating Acid-Dissociation Constants of Proteins Using the Boundary Element Method
1997
Boundary integral methods for the Poisson equation of continuum dielectric solvation models
1997
Lattice-sum methods for calculating electrostatic interactions in molecular simulations
1995
Classical Electrostatics in Biology and Chemistry
1995 StandoutScience
Helix-helix interactions in lipid bilayers
1996
A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts
1998
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
1999 Standout
General parameterization of a reaction field theory combined with the boundary element method
1994
Continuum and Dipole-Lattice Models of Solvation
1997 StandoutNobel
Calculation of the reaction field due to off-center point multipoles
1997
Finite element approach to the electrostatics of macromolecules with arbitrary geometries
1993
Phosphate ester hydrolysis: calculation of gas-phase reaction paths and solvation effects
1994
A generalized reaction field method for molecular dynamics simulations
1995
GB/SA-Based Continuum Solvation Model for Octanol
1997
Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes
1997
Electrostatic Potentials inRhodopseudomonas viridisReaction Centers: Implications for the Driving Force and Directionality of Electron Transfer
1996
Solvent effects on molecular spectra. III. Absorption to and emission from the lowest singlet (n,π*) state of dilute pyrimidine in water
1993
A General Treatment of Solvent Effects Based on Screened Coulomb Potentials
2000
Potential of mean force calculation of solute molecules in water by a modified solvent-accessible surface method
1997
Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-microscopic and Microscopic Approaches
1997 StandoutNobel
Electrostatics of nanosystems: Application to microtubules and the ribosome
2001 Standout
NAMD2: Greater Scalability for Parallel Molecular Dynamics
1999 Standout
Energy correction to simulation of volume polarization in reaction field theory
2002
Quantum mechanical geometry optimization in solution using a finite element continuum electrostatics method
1996
Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems
1996
Solvation Free Energies of Peptides: Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson−Boltzmann Equation
1997
Atomic Structure of the DNA Repair [4Fe-4S] Enzyme Endonuclease III
1992 Science
Statistical Mechanics of a Multipolar Gas: A Lattice Field Theory Approach
1996
Screened Coulomb potential based implicit solvent model: Formulation and parameter development
1998
Continuum Electrostatics Model for Ion Solvation and Relative Acidity of HCl in Supercritical Water
1996
Charge penetration in dielectric models of solvation
1997
A Comprehensive Analytical Treatment of Continuum Electrostatics
1996
A stringent test of the cavity concept in continuum dielectrics
1997 StandoutNobel
Progress in Modeling of Protein Structures and Interactions
2005 StandoutScienceNobel
Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions
1997
Molecular dynamics simulation with a continuum electrostatic model of the solvent
1995
Computer Simulation of Protein−Protein Interactions
2001
Protein Structure Prediction and Structural Genomics
2001 StandoutScienceNobel
Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies
2008 StandoutNobel
The Effect of Solvent Density Inhomogeneities on Solute Dynamics in Supercritical Fluids: A Theoretical Perspective
1998
A Compressible Continuum Model Study of the Chloride plus Methyl Chloride Reaction in Supercritical Water
1997
Polarizable continuum model calculations including electron correlation in the ab initio wavefunction
1993
A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent
1997
Charge Screening and the Dielectric Constant of Proteins: Insights from Molecular Dynamics
1996
Electrostatic Basis for Enzyme Catalysis
2006 StandoutNobel
ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
1994
How Well Does Poisson−Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis
2006
Novel generalized Born methods
2002
Development and parametrization of continuum solvent models. I. Models based on the boundary element method
1996
Calculation of the aqueous solvation free energy of the proton
1998
A Continuum Solvation Model Including Electrostriction: Application to the Anisole Hydrolysis Reaction in Supercritical Water
1996
Numerical solution of the nonlinear Poisson–Boltzmann equation: Developing more robust and efficient methods
1995
Solvation energies and electronic spectra in polar, polarizable media: Simulation tests of dielectric continuum theory
1996
Reaction field spectral shifts with semiempirical molecular orbital theory
1997
Fast Boundary Element Method for the Linear Poisson−Boltzmann Equation
2002
Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions
2000
The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers
2001
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
A quantum mechanical-Poisson–Boltzmann equation approach for studying charge flow between ions and a dielectric continuum
2000
The solvation reaction field for a hydrogen atom in a dielectric continuum
1996
Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
1993 StandoutNobel
Electrostatic interactions in macromolecules
1994
Calculation of Relative Binding Free Energies of Peptidic Inhibitors to HIV-1 Protease and Its I84V Mutant
1998
The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems
1995
pKaCalculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations: A Quantitative Test of QM/MM Protocols
2005
The Cavity and Pore Helices in the KcsA K + Channel: Electrostatic Stabilization of Monovalent Cations
1999 StandoutScienceNobel
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
2005
Quantum Mechanical Continuum Solvation Models
2005 Standout
Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
1998
Incorporating solvent and ion screening into molecular dynamics using the finite‐difference Poisson–Boltzmann method
1991
Dielectric and thermodynamic response of a generalized reaction field model for liquid state simulations
1993
A Poisson–Boltzmann dynamics method with nonperiodic boundary condition
2003
Influence of Artificial Periodicity and Ionic Strength in Molecular Dynamics Simulations of Charged Biomolecules Employing Lattice-Sum Methods
2003
Solution of the linearized Poisson–Boltzmann equation
2004
A model of a local dielectric constant in proteins
1998
Calculation of Dielectric Constants near Polyelectrolytes in Solution
1997
Structural insights into TRPM8 inhibition and desensitization
2019 StandoutScienceNobel
Solvation Free Energies Estimated from Macroscopic Continuum Theory: An Accuracy Assessment
1994
Using a Charging Coordinate in Studies of Ionization Induced Partial Unfolding
2006 StandoutNobel
A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation
1991
Grid positioning independence and the reduction of self‐energy in the solution of the Poisson—Boltzmann equation
1993
A simple physical model for binding energy hot spots in protein–protein complexes
2002 StandoutNobel
Diffusion approach to the linear Poisson–Boltzmann equation
1998
Molecular properties in solution described with a continuum solvation model
2002
Calculation of Alkane to Water Solvation Free Energies Using Continuum Solvent Models
1996
A smooth particle mesh Ewald method
1995 Standout
Works of Malcolm E. Davis being referenced
Combined Conformational Search and Finite-Difference Poisson?Boltzmann Approach for Flexible Docking
1994
Simulation of enzyme–substrate encounter with gated active sites
1994
Poisson-Boltzmann analysis of the lambda repressor-operator interaction
1992
Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme
1993
Empirical free energy calculations: a blind test and further improvements to the method
1997
The inducible multipole solvation model: A new model for solvation effects on solute electrostatics
1994
Solving the finite difference linearized Poisson‐Boltzmann equation: A comparison of relaxation and conjugate gradient methods
1989
A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems
1994
Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program
1995
[22] Diffusion-controlled enzymatic reactions
1991
Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence
1991
Electric-field distribution inside the bacterial photosynthetic reaction center of Rhodopseudomonas viridis
1990
Electrostatics in biomolecular structure and dynamics. [Erratum to document cited in CA112(25):231952j]
1993
Electrostatic energy calculations by a Finite‐difference method: Rapid calculation of charge–solvent interaction energies
1992
Brownian dynamics simulations of diffusional encounters between triose phosphate isomerase and glyceraldehyde phosphate: electrostatic steering of glyceraldehyde phosphate
1993
Solving the finite‐difference non‐linear Poisson–Boltzmann equation
1992
Electrostatics in biomolecular structure and dynamics
1990
Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
1993
Finite difference Poisson-Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing
1997
Calculating electrostatic forces from grid‐calculated potentials
1990
Implementation of a six-dimensional search using theAMoRetranslation function for difficult molecular-replacement problems
1999
Continuum model calculations of solvation free energies: accurate evaluation of electrostatic contributions
1992
Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program
1991