Standout Papers
Citation Impact
Citing Papers
AB INITIO QUANTUM CHEMICAL AND MIXED QUANTUM MECHANICS/MOLECULAR MECHANICS (QM/MM) METHODS FOR STUDYING ENZYMATIC CATALYSIS
2005
Crystal Structure of a Lipid G Protein–Coupled Receptor
2012 Science
Protein interaction networks revealed by proteome coevolution
2019 StandoutScienceNobel
Protein homology model refinement by large-scale energy optimization
2018 StandoutNobel
Voltage sensor conformations in the open and closed states in rosetta structural models of K + channels
2006 StandoutNobel
Origins of coevolution between residues distant in protein 3D structures
2017 StandoutNobel
Simultaneous prediction of protein folding and docking at high resolution
2009 StandoutNobel
Protein structure determination using metagenome sequence data
2017 StandoutScienceNobel
Sculpting conducting nanopore size and shape through de novo protein design
2024 StandoutScienceNobel
Structural implications of hERG K+ channel block by a high-affinity minimally structured blocker
2018
Expansive discovery of chemically diverse structured macrocyclic oligoamides
2024 StandoutScienceNobel
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
Refinement of protein termini in template‐based modeling using conformational space annealing
2011
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
2008
Charge Delocalization in Proton Channels, I: The Aquaporin Channels and Proton Blockage
2006
Enhanced Concentration of Polarizable Anions at the Liquid Water Surface: SHG Spectroscopy and MD Simulations of Sodium Thiocyanide
2005
Improved molecular replacement by density- and energy-guided protein structure optimization
2011 StandoutNatureNobel
A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity
2014 StandoutNobel
X-Ray Structure of Acid-Sensing Ion Channel 1–Snake Toxin Complex Reveals Open State of a Na+-Selective Channel
2014 StandoutNobel
Kinetics and Mechanism of Proton Transport across Membrane Nanopores
2006
High-resolution crystal structure of human protease-activated receptor 1
2012 StandoutNatureNobel
Conformer generation under restraints
2006
The Cryo-EM Structure of a Translation Initiation Complex from Escherichia coli
2005 StandoutNobel
The Two Na+ Sites in the Human Serotonin Transporter Play Distinct Roles in the Ion Coupling and Electrogenicity of Transport
2013
The dynamic disulphide relay of quiescin sulphydryl oxidase
2012 StandoutNatureNobel
Transient water wires mediate selective proton transport in designed channel proteins
2023
New potential binding determinant for hERG channel inhibitors
2016
Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation
2006
Molecular Dynamics Simulation for All
2018 Standout
A structure-based computational workflow to predict liability and binding modes of small molecules to hERG
2020 StandoutNobel
A heteromeric Texas coral snake toxin targets acid-sensing ion channels to produce pain
2011 StandoutNatureNobel
Protein Structure Modeling with MODELLER
2008 Standout
Computational studies of proton transport through the M2 channel
2003
UCSF Chimera—A visualization system for exploratory research and analysis
2004 Standout
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
Redox-coupled proton pumping in cytochrome c oxidase: Further insights from computer simulation
2007
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
2009
A Cell-Penetrating Scorpion Toxin Enables Mode-Specific Modulation of TRPA1 and Pain
2019 StandoutNobel
About the choice of the protogenic group in polymer electrolyte membranes: Ab initio modelling of sulfonic acid, phosphonic acid, and imidazole functionalized alkanes
2006
De novo design of a fluorescence-activating β-barrel
2018 StandoutNatureNobel
Structural snapshots of TRPV1 reveal mechanism of polymodal functionality
2021 StandoutNobel
Molecular Determinants of hERG Channel Block by Terfenadine and Cisapride
2008
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
2006 StandoutNobel
RosettaLigand Docking with Full Ligand and Receptor Flexibility
2008 StandoutNobel
On the origin of the electrostatic barrier for proton transport in aquaporin
2004 StandoutNobel
Toward a Consensus Model of the hERG Potassium Channel
2010
Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction
2008
Computational Modeling of the Catalytic Reaction in Triosephosphate Isomerase
2004
Proton transport in functionalised additives for PEM fuel cells: contributions from atomistic simulations
2012
ModBase, a database of annotated comparative protein structure models, and associated resources
2010
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
2009 Standout
Proton Transport through Water-Filled Carbon Nanotubes
2003
Ranolazine inhibition of hERG potassium channels: Drug–pore interactions and reduced potency against inactivation mutants
2014
Toward high-resolution prediction and design of transmembrane helical protein structures
2007 StandoutNobel
Specific Ion Effects at the Air/Water Interface
2005 Standout
ON THE NATURE OF IONS AT THE LIQUID WATER SURFACE
2005
Transport in Proton Conductors for Fuel-Cell Applications: Simulations, Elementary Reactions, and Phenomenology
2004 Standout
Structural Insight into Nascent Polypeptide Chain–Mediated Translational Stalling
2009 StandoutScienceNobel
The emerging role of computational design in peptide macrocycle drug discovery
2020
Structure-based characterization of novel TRPV5 inhibitors
2019
Water as an Active Constituent in Cell Biology
2007 Standout
Proton binding within a membrane protein by a protonated water cluster
2005
Acid activation mechanism of the influenza A M2 proton channel
2016
Unified Molecular Picture of the Surfaces of Aqueous Acid, Base, and Salt Solutions
2005
Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-Centered Density Matrix Propagation (ADMP) Approach
2004
De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity
2016 StandoutScienceNobel
A model of anthrax toxin lethal factor bound to protective antigen
2005 StandoutNobel
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase
2008 StandoutNobel
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes
2006 Standout
Sequence optimization and designability of enzyme active sites
2005
Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking
2021 StandoutNobel
Accurate protein structure modeling using sparse NMR data and homologous structure information
2012 StandoutNobel
Protein Side-Chain Motion and Hydration in Proton-Transfer Pathways. Results for Cytochrome P450cam
2003
Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1
2021 StandoutNobel
Generalized ensemble methods for de novo structure prediction
2009 StandoutNobel
Sum-Frequency Vibrational Spectroscopy on Water Interfaces: Polar Orientation of Water Molecules at Interfaces
2006 Standout
Progress in Modeling of Protein Structures and Interactions
2005 StandoutScienceNobel
Computational protein structure refinement: almost there, yet still so far to go
2017
Monte Carlo simulations of proton pumps: On the working principles of the biological valve that controls proton pumping in cytochrome c oxidase
2006 StandoutNobel
Comparative Protein Structure Modeling Using MODELLER
2007 Standout
Molecular Determinants of Selectivity and Efficacy at the Dopamine D3 Receptor
2012
Inherent Proton Conduction in a 2D Coordination Framework
2012 StandoutNobel
Electrostatic Basis for Enzyme Catalysis
2006 StandoutNobel
Water surface is acidic
2007
Prediction of membrane protein structures with complex topologies using limited constraints
2009 StandoutNobel
Elementary Steps in Excited-State Proton Transfer
2004
Postsynthesis Modification of a Porous Coordination Polymer by LiCl To Enhance H+ Transport
2013 StandoutNobel
Calculation of Protein-Ligand Binding Affinities
2007
Thermal Equilibrium of High- and Low-Spin Forms of Cytochrome P450 BM-3: Repositioning of the Substrate?
2005
Evidence for an Enhanced Hydronium Concentration at the Liquid Water Surface
2005
Development of Safe Drugs: The hERG Challenge
2017
Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics
2016
Assessing hERG Pore Models As Templates for Drug Docking Using Published Experimental Constraints: The Inactivated State in the Context of Drug Block
2014
Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples
2012 StandoutNobel
A bond-order analysis of the mechanism for hydrated proton mobility in liquid water
2004
Quantum Mechanical Continuum Solvation Models
2005 Standout
Structure and dynamics of concentrated hydrochloric acid solutions. A first principles molecular dynamics study
2004
A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles
2023
Prediction of Protein–Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations
2016
Computer simulation of explicit proton translocation in cytochrome c oxidase: The D-pathway
2005
The Good, the Bad, and the Twisted Revisited: An Analysis of Ligand Geometry in Highly Resolved Protein–Ligand X-ray Structures
2021
Sequence co-evolution gives 3D contacts and structures of protein complexes
2014
Modeling of Open, Closed, and Open-Inactivated States of the hERG1 Channel: Structural Mechanisms of the State-Dependent Drug Binding
2012
Lys49 myotoxin from the Brazilian lancehead pit viper elicits pain through regulated ATP release
2017 StandoutNobel
Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals
2006 StandoutNobel
Partitioning of atmospherically relevant ions between bulk water and the water/vapor interface
2006
hERG liability classification models using machine learning techniques
2019
Docking Model of Drug Binding to the Human Ether-à-go-go Potassium Channel Guided by Tandem Dimer Mutant Patch-Clamp Data: A Synergic Approach
2009
Comparative Protein Structure Modeling Using Modeller
2006 Standout
Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations
2007
Works of Tyler Day being referenced
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps
2018
A hierarchical approach to all‐atom protein loop prediction
2004 Standout
New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies
2006
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
2013 Standout
The properties of ion-water clusters. II. Solvation structures of Na+, Cl−, and H+ clusters as a function of temperature
2006
On the amphiphilic behavior of the hydrated proton: an ab initio molecular dynamics study
2005
Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling
2017
The Mechanism of Hydrated Proton Transport in Water
2000
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
2005 Standout
The Hydrated Proton at the Water Liquid/Vapor Interface
2004
A second generation multistate empirical valence bond model for proton transport in aqueous systems
2002
The properties of ion-water clusters. I. The protonated 21-water cluster
2005