Citation Impact
Citing Papers
Proton Binding to Proteins: p K a Calculations with Explicit and Implicit Solvent Models
2004
AB INITIO QUANTUM CHEMICAL AND MIXED QUANTUM MECHANICS/MOLECULAR MECHANICS (QM/MM) METHODS FOR STUDYING ENZYMATIC CATALYSIS
2005
Principles for designing proteins with cavities formed by curved β sheets
2017 StandoutScienceNobel
Global analysis of protein folding using massively parallel design, synthesis, and testing
2017 StandoutScienceNobel
Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O 2 activation
2019 StandoutNobel
Keeping G Proteins at Bay: A Complex Between G Protein-Coupled Receptor Kinase 2 and Gßγ
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Computational design of closely related proteins that adopt two well-defined but structurally divergent folds
2020 StandoutNobel
Structure of the Rotor Ring of F-Type Na + -ATPase from Ilyobacter tartaricus
2005 Science
The use of mRNA display to select high-affinity protein-binding peptides
2001 StandoutNobel
A minimal sequence code for switching protein structure and function
2009
The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components
2005 StandoutNobel
Protein stability promotes evolvability
2006 StandoutNobel
Ions and Counterions in a Biological Channel: A Molecular Dynamics Simulation of OmpF Porin from Escherichia coli in an Explicit Membrane with 1M KCl Aqueous Salt Solution
2002
Evaluation of a fast implicit solvent model for molecular dynamics simulations
2001
A server and database for dipole moments of proteins
2007
Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
1997
Atomic model of the type III secretion system needle
2012 StandoutNatureNobel
Constant pH molecular dynamics in generalized Born implicit solvent
2004
Modeling electrostatic effects in proteins
2006 StandoutNobel
Future directions for combining molecular and continuum models in protein simulations
1998
A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein–water interface as a determinant of pKavalues
2008
What are the dielectric “constants” of proteins and how to validate electrostatic models?
2001
Structure of the Type VI Secretion System Contractile Sheath
2015 StandoutNobel
A fast and simple method to calculate protonation states in proteins
1999
Irritant-evoked activation and calcium modulation of the TRPA1 receptor
2020 StandoutNatureNobel
Combining Conformational Flexibility and Continuum Electrostatics for Calculating pKas in Proteins
2002
Protein Dynamics Tightly Connected to the Dynamics of Surrounding and Internal Water Molecules
2006
Optimizing the hydrogen‐bond network in Poisson–Boltzmann equation‐based pKa calculations
2001
Applicability of a continuum solvation model to the octanol water transfer: CFF91 based model for amino acids
1995
The Mechanism and Pathway of pH Induced Swelling in Cowpea Chlorotic Mottle Virus
2002
Improving macromolecular electrostatics calculations
1999
Chapter 23 Solvent Denaturation of Proteins and Interpretations of the m Value
2009
Reactivity of Intein Thioesters: Appending a Functional Group to a Protein
2006
Theory of electrostatic interactions in macromolecules
1995
How Optimal Are the Binding Energetics of Barnase and Barstar?
2004
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
2012
Stabilization of Internal Charges in a Protein: Water Penetration or Conformational Change?
2004
Structures of Human Exonuclease 1 DNA Complexes Suggest a Unified Mechanism for Nuclease Family
2011 StandoutNobel
Electrostatic contributions to protein–protein binding affinities: Application to Rap/Raf interaction
1998 StandoutNobel
Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials
2003
Crystal structure of an acetylcholinesterase–fasciculin complex: interaction of a three-fingered toxin from snake venom with its target
1995
A Cell-Penetrating Scorpion Toxin Enables Mode-Specific Modulation of TRPA1 and Pain
2019 StandoutNobel
Type IV Pilus Structure by Cryo-Electron Microscopy and Crystallography: Implications for Pilus Assembly and Functions
2006
Implicit solvent models
1999
Conformational sampling for the impatient
2004
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
2004 Standout
Constant pH Molecular Dynamics with Proton Tautomerism
2005
Streptavidin-binding and -dimerizing ligands discovered by phage display, topochemistry, and structure-based design
1999
Experimental pKa Values of Buried Residues: Analysis with Continuum Methods and Role of Water Penetration
2002
Structural snapshots of TRPV1 reveal mechanism of polymodal functionality
2021 StandoutNobel
Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility
1995
Structure of the DNA Repair and Replication Endonuclease and Exonuclease FEN-1
1998
Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis
1996 Nobel
Electrostatic effects in macromolecules: fundamental concepts and practical modeling
1998 StandoutNobel
Understanding photosynthetic light-harvesting: a bottom up theoretical approach
2013
Quantitative reactivity profiling predicts functional cysteines in proteomes
2010 StandoutNatureNobel
Biophysical Studies of eIF4E Cap-binding Protein: Recognition of mRNA 5′ Cap Structure and Synthetic Fragments of eIF4G and 4E-BP1 Proteins
2002
Variability in the pKa of histidine side‐chains correlates with burial within proteins
2002
Relation Between Protein Stability, Evolution and Structure, as Probed by Carboxylic Acid Mutations
2004
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid
2008
Electrostatic Contributions to the Binding Free Energy of the λcI Repressor to DNA
1998
A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins
2000
Explicit solvent models in protein pKa calculations
1996
Electrostatic aspects of protein–protein interactions
2000
High Apparent Dielectric Constant Inside a Protein Reflects Structural Reorganization Coupled to the Ionization of an Internal Asp
2006
Electrostatic Contributions to T4 Lysozyme Stability: Solvent-Exposed Charges versus Semi-Buried Salt Bridges
2002
Are Acidic and Basic Groups in Buried Proteins Predicted to be Ionized?
2005
Prediction of functionally important residues based solely on the computed energetics of protein structure 1 1Edited by B. Honig
2001
Elucidating the Folding Problem of Helical Peptides using Empirical Parameters. III>Temperature and pH Dependence
1995
Titration Behavior of Residues at the Entrance of the D-Pathway of Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Continuum Electrostatic Calculations
2005 Nobel
Constant‐pH molecular dynamics using continuous titration coordinates
2004
On the importance of being zwitterionic: enzymatic catalysis of decarboxylation and deprotonation of cationic carbon
2004
Chemical synthesis and binding activity of the trypanosomatid cap-4 structure
2004
A critical analysis of continuum electrostatics: The screened Coulomb potential–implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins
2002
Poisson–Boltzmann Methods for Biomolecular Electrostatics
2004
Toward high-resolution prediction and design of transmembrane helical protein structures
2007 StandoutNobel
Quantitative exploration of the molecular origin of the activation of GTPase
2013 StandoutNobel
Ewald artifacts in computer simulations of ionic solvation and ion–ion interaction: A continuum electrostatics study
1999
Exploring the nature of the translocon-assisted protein insertion
2012 StandoutNobel
Dynamical Contributions to Enzyme Catalysis: Critical Tests of A Popular Hypothesis
2006 StandoutNobel
Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome
2011 StandoutNobel
Electrostatics and dynamics of proteins
2003
A fast and Space-efficient boundary element method for computing electrostatic and hydration effects in large molecules
1996
Nonlocal dielectric functions on the nanoscale: Screened forces from unscreened potentials
2003
Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems
2000
CHARMM‐GUI: A web‐based graphical user interface for CHARMM
2008 Standout
pKa Calculations with QM/MM Free Energy Perturbations
2003
Calculation of HyHel10-lysozyme binding free energy changes: Effect of ten point mutations
1998
The Deacylation Step of Acetylcholinesterase: Computer Simulation Studies
2000
pKa Shifts in Small Molecules and HIV Protease: Electrostatics and Conformation
1998
Ultrafast solvation dynamics at binding and active sites of photolyases
2010 StandoutNobel
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
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
1999 Standout
Self-Consistent, Free Energy Based Approximation To Calculate pH Dependent Electrostatic Effects in Proteins
1996
COMPUTER SIMULATIONS WITH EXPLICIT SOLVENT: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects
1998
Electrostatics and the Gating Pore of Shaker Potassium Channels
2001
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase
2008 StandoutNobel
A General Treatment of Solvent Effects Based on Screened Coulomb Potentials
2000
Solvent dramatically affects protein structure refinement
2008 StandoutNobel
Robust excitons inhabit soft supramolecular nanotubes
2014 StandoutNobel
Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-microscopic and Microscopic Approaches
1997 StandoutNobel
Realistic simulation of the activation of voltage-gated ion channels
2012 StandoutNobel
Freeze-frame inhibitor captures acetylcholinesterase in a unique conformation
2004 StandoutNobel
Progress in Modeling of Protein Structures and Interactions
2005 StandoutScienceNobel
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
2003 StandoutNobel
Molecular dynamics simulation with a continuum electrostatic model of the solvent
1995
Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models
2005
Monte Carlo simulations of proton pumps: On the working principles of the biological valve that controls proton pumping in cytochrome c oxidase
2006 StandoutNobel
DFT/Electrostatic Calculations of pKa Values in Cytochrome c Oxidase
2005
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 Solution Structure and Dynamics of the Pleckstrin Homology Domain of G Protein-coupled Receptor Kinase 2 (β-Adrenergic Receptor Kinase 1)
1998
Charge Screening and the Dielectric Constant of Proteins: Insights from Molecular Dynamics
1996
Nickel Superoxide Dismutase Structure and Mechanism
2004
Electrostatic Basis for Enzyme Catalysis
2006 StandoutNobel
Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F 0 -ATPase
2012 StandoutNobel
Calculated Protein and Proton Motions Coupled to Electron Transfer: Electron Transfer from QA- to QB in Bacterial Photosynthetic Reaction Centers
1999
Development and parametrization of continuum solvent models. I. Models based on the boundary element method
1996
Fast Boundary Element Method for the Linear Poisson−Boltzmann Equation
2002
Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase
2003 StandoutNobel
Accurate, conformation-dependent predictions of solvent effects on protein ionization constants
2007
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
Quantum Mechanical Continuum Solvation Models
2005 Standout
Including Side Chain Flexibility in Continuum Electrostatic Calculations of Protein Titration
1996
How important are entropic contributions to enzyme catalysis?
2000 StandoutNobel
pKa of Residue 66 in Staphylococal nuclease. I. Insights from QM/MM Simulations with Conventional Sampling
2008
Computational design of a pH-sensitive IgG binding protein
2013 StandoutNobel
Cu-Catalyzed Azide−Alkyne Cycloaddition
2008 StandoutNobel
A model of a local dielectric constant in proteins
1998
Review: Protein Design—Where We Were, Where We Are, Where We're Going
2001
Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides.
1991
Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases
2009 StandoutNobel
De novo design of protein logic gates
2020 StandoutScienceNobel
On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes
2010 StandoutNobel
Cap-Independent Translation Is Required for Starvation-Induced Differentiation in Yeast
2007 StandoutScienceNobel
A simple physical model for binding energy hot spots in protein–protein complexes
2002 StandoutNobel
Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
2010 StandoutNobel
Structural basis for gating charge movement in the voltage sensor of a sodium channel
2011 StandoutNobel
Works of Jan Antosiewicz being referenced
Computing ionization states of proteins with a detailed charge model
1996
Prediction of Ph-dependent Properties of Proteins
1994
Charge–Charge Interactions are Key Determinants of the pK Values of Ionizable Groups in Ribonuclease Sa (pI=3.5) and a Basic Variant (pI=10.2)
2003
Prediction of Secondary Ionization of the Phosphate Group in Phosphotyrosine Peptides
2003
Simulation of charge-mutant acetylcholinesterases
1995
Electrostatics of hemoglobins from measurements of the electric dichroism and computer simulations
1995
Thermodynamic linkage between the binding of protons and inhibitors to HIV‐1 protease
1999
Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories
1997
Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand
1995
Computation of the dipole moments of proteins
1995
Empirical relationships between protein structure and carboxyl pKa values in proteins
2002
Langevin dynamics of proteins at constantp H
2002
The nature of protein dipole moments: experimental and calculated permanent dipole of .alpha.-chymotrypsin
1989
Stopped-flow and Brownian dynamics studies of electrostatic effects in the kinetics of binding of 7-methyl-GpppG to the protein eIF4E
2000
Constant-pH molecular dynamics simulations: a test case of succinic acid
2004
Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program
1995
pKa Measurements from Nuclear Magnetic Resonance for the B1 and B2 Immunoglobulin G-Binding Domains of Protein G: Comparison with Calculated Values for Nuclear Magnetic Resonance and X-ray Structures
1997
Acetylcholinesterase: Effects of Ionic Strength and Dimerization on the Rate Constants
1994
The Determinants of pKas in Proteins
1996
Effects of pH on kinetics of binding of mRNA-cap analogs by translation initiation factor eIF4E
2003
Theoretical and Experimental Analysis of Ionization Equilibria in Ovomucoid Third Domain
1998