Standout Papers
- CHARMM‐GUI: A web‐based graphical user interface for CHARMM (2008)
- CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field (2015)
- CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations (2014)
- Generation and application of new rat monoclonal antibodies against synthetic FLAG and OLLAS tags for improved immunodetection (2007)
Citation Impact
Citing Papers
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
De novo design of transmembrane β barrels
2021 StandoutScienceNobel
Protein structure determination using metagenome sequence data
2017 StandoutScienceNobel
Accurate computational design of multipass transmembrane proteins
2018 StandoutScienceNobel
Designed protein logic to target cells with precise combinations of surface antigens
2020 StandoutScienceNobel
A Light-Actuated Nanovalve Derived from a Channel Protein
2005 StandoutScienceNobel
Sculpting conducting nanopore size and shape through de novo protein design
2024 StandoutScienceNobel
Cutting Edge: Langerin/CD207 Receptor on Dendritic Cells Mediates Efficient Antigen Presentation on MHC I and II Products In Vivo
2008 StandoutNobel
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria
2020
Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism
2024 StandoutNobel
Graphene Symmetry Amplified by Designed Peptide Self-Assembly
2016
Bilayer-Mediated Structural Transitions Control Mechanosensitivity of the TREK-2 K2P Channel
2017
Treml4, an Ig Superfamily Member, Mediates Presentation of Several Antigens to T Cells In Vivo, Including Protective Immunity to HER2 Protein
2011 StandoutNobel
PACKMOL : A package for building initial configurations for molecular dynamics simulations
2009 Standout
OPM database and PPM web server: resources for positioning of proteins in membranes
2011
The open pore conformation of potassium channels
2002 StandoutNatureNobel
Structural Basis for Gating and Activation of RyR1
2016 StandoutNobel
A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing
2007
Force Fields for Protein Simulations
2003
Discoveries in structure and physiology of mechanically activated ion channels
2020 StandoutNatureNobel
QM/MM Methods for Biomolecular Systems
2009 Standout
Atomic model of the type III secretion system needle
2012 StandoutNatureNobel
Modeling electrostatic effects in proteins
2006 StandoutNobel
Channel opening and gating mechanism in AMPA-subtype glutamate receptors
2017 StandoutNatureNobel
Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes
2024 StandoutNobel
Structural Determinants of Proton Blockage in Aquaporins
2004
DOCK 6: Combining techniques to model RNA–small molecule complexes
2009
The Transmembrane Domain Mediates Tetramerization of α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors
2016
Toward the active conformations of rhodopsin and the β2‐adrenergic receptor
2004
Empirical force fields for biological macromolecules: Overview and issues
2004
Atomistic mechanism for the activation and desensitization of an AMPA-subtype glutamate receptor
2011
Integrins Form an Expanding Diffusional Barrier that Coordinates Phagocytosis
2016 StandoutNobel
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
2004
Outer membrane protein folding from an energy landscape perspective
2017
The road to fully programmable protein catalysis
2022 StandoutNatureNobel
Inhibition of α-helix-mediated protein–protein interactions using designed molecules
2013
Transient water wires mediate selective proton transport in designed channel proteins
2023
Protein refolding is required for assembly of the type three secretion needle
2010
Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution
2012 StandoutNobel
The Amber biomolecular simulation programs
2005 Standout
Principles for designing ideal protein structures
2012 StandoutNatureNobel
An exciting but challenging road ahead for computational enzyme design
2010 StandoutNobel
Structure of the KcsA channel intracellular gate in the open state.
2001
Constructing ion channels from water-soluble α-helical barrels
2021
Microbial Stimulation Fully Differentiates Monocytes to DC-SIGN/CD209+ Dendritic Cells for Immune T Cell Areas
2010 StandoutNobel
A Gate in the Selectivity Filter of Potassium Channels
2005
Improved sampling methods for molecular simulation
2007
A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells
2014 StandoutNobel
The coming of age of de novo protein design
2016 StandoutNatureNobel
Exploring protein native states and large‐scale conformational changes with a modified generalized born model
2004 Standout
Structure of the mechanically activated ion channel Piezo1
2017 StandoutNatureNobel
Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue GltTk
2016
TRPV1 structures in distinct conformations reveal activation mechanisms
2013 StandoutNatureNobel
Recent advances in implicit solvent-based methods for biomolecular simulations
2008
Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores
2019
Transmembrane Pickets Connect Cyto- and Pericellular Skeletons Forming Barriers to Receptor Engagement
2018 StandoutNobel
Computational redesign of endonuclease DNA binding and cleavage specificity
2006 StandoutNatureNobel
Accelerated Poisson–Boltzmann calculations for static and dynamic systems
2002
Polarization effects and charge transfer in the KcsA potassium channel
2006
The Structure of the Salmonella typhimurium Type III Secretion System Needle Shows Divergence from the Flagellar System
2010
De novo design of bioactive protein switches
2019 StandoutNatureNobel
Structural snapshots of TRPV1 reveal mechanism of polymodal functionality
2021 StandoutNobel
Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating
2017
New monoclonal anti-mouse DC-SIGN antibodies reactive with acetone-fixed cells
2010 StandoutNobel
Recent advances in the development and application of implicit solvent models in biomolecule simulations
2004
Crystal structure of the µ-opioid receptor bound to a morphinan antagonist
2012 StandoutNatureNobel
Theoretical and Computational Protein Design
2011
X-ray structures define human P2X3 receptor gating cycle and antagonist action
2016 Nature
Physical mechanism for gating and mechanosensitivity of the human TRAAK K+ channel
2014 NatureNobel
Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study
2008 StandoutNobel
Simulations of ion current in realistic models of ion channels: The KcsA potassium channel
2002 StandoutNobel
Controlling protein assembly on inorganic crystals through designed protein interfaces
2019 StandoutNatureNobel
Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I
2020
Computational design of ligand-binding proteins with high affinity and selectivity
2013 StandoutNatureNobel
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
2009 Standout
Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane
2020
STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures
2011
Poisson–Boltzmann Methods for Biomolecular Electrostatics
2004
Toward high-resolution prediction and design of transmembrane helical protein structures
2007 StandoutNobel
Elucidation of AMPA receptor–stargazin complexes by cryo–electron microscopy
2016 StandoutScienceNobel
Molecular Determinants of Bim(BH3) Peptide Binding to Pro-Survival Proteins
2012
Computer Simulation of Liquids
2017 Standout
Electrostatics and dynamics of proteins
2003
Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold
2011 StandoutScienceNobel
Structure of the STRA6 receptor for retinol uptake
2016 StandoutScienceNobel
A structural model of the active ribosome-bound membrane protein insertase YidC
2014
Constitutive Activation of the Shaker Kv Channel
2003
Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase
2006
Incorporating variable dielectric environments into the generalized Born model
2005
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
1999 Standout
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures
2014 StandoutNobel
A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations
2020
Outer Membrane Biogenesis
2017
Efficiency and Accuracy of the Generalized Solvent Boundary Potential for Hybrid QM/MM Simulations: Implementation for Semiempirical Hamiltonians
2008
Bacterial machineries for the assembly of membrane-embedded β-barrel proteins
2018
Novel Kinetic Intermediates Populated along the Folding Pathway of the Transmembrane β-Barrel OmpA
2016
Progress in Modeling of Protein Structures and Interactions
2005 StandoutScienceNobel
Structure of mouse protocadherin 15 of the stereocilia tip link in complex with LHFPL5
2018
Computational design of mechanically coupled axle-rotor protein assemblies
2022 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
ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution
2019
Calculation of Protein-Ligand Binding Affinities
2007
Molecular basis of force-from-lipids gating in the mechanosensitive channel MscS
2019
Barriers to the free diffusion of proteins and lipids in the plasma membrane
2015
What's the point of the type III secretion system needle?
2008
“Proton Holes” in Long-Range Proton Transfer Reactions in Solution and Enzymes: A Theoretical Analysis
2006
Update 1 of: Computational Modeling Approaches to Structure–Function Analysis of G Protein-Coupled Receptors
2011
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
2005
Fast Parallel Algorithms for Short-Range Molecular Dynamics
1995 Standout
Polarizable Force Fields: History, Test Cases, and Prospects
2007 StandoutNobel
pKa of Residue 66 in Staphylococal nuclease. I. Insights from QM/MM Simulations with Conventional Sampling
2008
A Poisson–Boltzmann dynamics method with nonperiodic boundary condition
2003
Antibody to Langerin/CD207 localizes large numbers of CD8α + dendritic cells to the marginal zone of mouse spleen
2009 StandoutNobel
Variational Electrostatic Projection (VEP) Methods for Efficient Modeling of the Macromolecular Electrostatic and Solvation Environment in Activated Dynamics Simulations
2004
pKa Analysis for the Zinc-Bound Water in Human Carbonic Anhydrase II: Benchmark for “Multiscale” QM/MM Simulations and Mechanistic Implications
2007
Works of Wonpil Im being referenced
Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
2007
A Grand Canonical Monte Carlo–Brownian Dynamics Algorithm for Simulating Ion Channels
2000
E. coli Outer Membrane and Interactions with OmpLA
2014
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
Theoretical and computational models of biological ion channels
2004
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
2003
Membrane Assembly of Simple Helix Homo-Oligomers Studied via Molecular Dynamics Simulations
2006
Application of torsion angle molecular dynamics for efficient sampling of protein conformations
2005
An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins
2003
BamA POTRA Domain Interacts with a Native Lipid Membrane Surface
2016
Optimized atomic radii for protein continuum electrostatics solvation forces
1999
Ion Permeation through the α-Hemolysin Channel: Theoretical Studies Based on Brownian Dynamics and Poisson-Nernst-Plank Electrodiffusion Theory
2004
Web interface for brownian dynamics simulation of ion transport and its applications to beta‐barrel pores
2011
Generation and application of new rat monoclonal antibodies against synthetic FLAG and OLLAS tags for improved immunodetection
2007 StandoutNobel
Generalized born model with a simple smoothing function
2003
Refinement of OprH-LPS Interactions by Molecular Simulations
2017
CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes
2009
Differences in the Electrostatic Surfaces of the Type III Secretion Needle Proteins PrgI, BsaL, and MxiH
2007
Bilayer Properties of Lipid A from Various Gram-Negative Bacteria
2016
Influence of Hydrophobic Mismatch on Structures and Dynamics of Gramicidin A and Lipid Bilayers
2012
Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability
2016
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling
2005
De novo Folding of Membrane Proteins: An Exploration of the Structure and NMR Properties of the fd Coat Protein
2004
Physical Properties of Bacterial Outer Membrane Models: Neutron Reflectometry & Molecular Simulation
2019
Implicit solvation based on generalized Born theory in different dielectric environments
2003
Simulation Study of Occk5 Functional Properties in Pseudomonas aeruginosa Outer Membranes
2018
Heterogeneity in non‐epitope loop sequence and outer membrane protein complexes alters antibody binding to the major porin protein PorB in serogroup B Neisseria meningitidis
2017
CHARMM‐GUI: A web‐based graphical user interface for CHARMM
2008 Standout
Ion Channels, Permeation, and Electrostatics: Insight into the Function of KcsA
2000
CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations
2014 Standout
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
2015 Standout
Novel Pyrrolopyrimidine-Based α-Helix Mimetics: Cell-Permeable Inhibitors of Protein−Protein Interactions
2010
Electrostatic free energy calculations using the generalized solvent boundary potential method
2002
Modeling of Specific Lipopolysaccharide Binding Sites on a Gram-Negative Porin
2019
How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets?
2015
Refinement of NMR Structures Using Implicit Solvent and Advanced Sampling Techniques
2004
Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry
2001
Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field
2006
Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
1998
Generalized solvent boundary potential for computer simulations
2001
Evidence for a fence that impedes the diffusion of phosphatidylinositol 4,5-bisphosphate out of the forming phagosomes of macrophages
2011