Citation Impact
Citing Papers
Experimental accuracy in protein structure refinement via molecular dynamics simulations
2018
An enumerative algorithm for de novo design of proteins with diverse pocket structures
2020 StandoutNobel
Generation of ordered protein assemblies using rigid three-body fusion
2021 StandoutNobel
Atomic-Level Characterization of the Structural Dynamics of Proteins
2010 StandoutScienceNobel
Consistent blind protein structure generation from NMR chemical shift data
2008 StandoutNobel
Protein homology model refinement by large-scale energy optimization
2018 StandoutNobel
Computational design of closely related proteins that adopt two well-defined but structurally divergent folds
2020 StandoutNobel
Protein structure determination using metagenome sequence data
2017 StandoutScienceNobel
Physically realistic homology models built with rosetta can be more accurate than their templates
2006 StandoutNobel
Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality
2020 StandoutNobel
Crystal Structure-Based Virtual Screening for Fragment-like Ligands of the Human Histamine H 1 Receptor
2011
Computational Stabilization of a Non‐Heme Iron Enzyme Enables Efficient Evolution of New Function
2024 StandoutNobel
Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4
2015 StandoutNobel
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
Refinement of protein termini in template‐based modeling using conformational space annealing
2011
SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation That Contributes Markedly to Stability
2009 StandoutNobel
Soft corrugated channel with synergistic exclusive discrimination gating for CO2 recognition in gas mixture
2023 StandoutNobel
GPCR activation mechanisms across classes and macro/microscales
2021
Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs
2019 StandoutNobel
SHARPEN—Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network
2009
Beware of docking!
2014
Dynamic personalities of proteins
2007 StandoutNature
Modeling electrostatic effects in proteins
2006 StandoutNobel
Can molecular dynamics simulations provide high‐resolution refinement of protein structure?
2007
A Powerful Hydrogen‐Bond‐Donating Organocatalyst for the Enantioselective Intramolecular Oxa‐Michael Reaction of α,β‐Unsaturated Amides and Esters
2013
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch
2009
Computational Enzyme Design
2013 StandoutNobel
Electrostatics calculations: latest methodological advances
2006
DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility
2009
Challenges and advances in computational docking: 2009 in review
2010
DRESS: a database of REfined solution NMR structures
2004
Protein structure prediction: when is it useful?
2009
Improved protein structure refinement guided by deep learning based accuracy estimation
2021 StandoutNobel
Improved sampling methods for molecular simulation
2007
High-resolution structure prediction and the crystallographic phase problem
2007 StandoutNatureNobel
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles
2016
Structure-based drug screening for G-protein-coupled receptors
2012 StandoutNobel
Structural basis of human ghrelin receptor signaling by ghrelin and the synthetic agonist ibutamoren
2021
Design of biologically active binary protein 2D materials
2021 StandoutNatureNobel
An enzyme-coupled biosensor enables (S)-reticuline production in yeast from glucose
2015
Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites
2021 StandoutNobel
Sequence-based prediction of protein domains
2004
Recent advances in implicit solvent-based methods for biomolecular simulations
2008
Improved protein structure prediction using potentials from deep learning
2020 StandoutNatureNobel
Progress and challenges in high‐resolution refinement of protein structure models
2005 StandoutNobel
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM
2009 StandoutNobel
Assessment of the protein‐structure refinement category in CASP8
2009
The Protein Structure Initiative: achievements and visions for the future
2012
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
2006 StandoutNobel
KoBaMIN: a knowledge-based minimization web server for protein structure refinement
2012 StandoutNobel
Refinement of protein structure homology models via long, all‐atom molecular dynamics simulations
2012
The SWISS-MODEL Repository: new features and functionalities
2005
Creation of an Amino Acid Network of Structurally Coupled Residues in the Directed Evolution of a Thermostable Enzyme
2009
Ligand–receptor interaction platforms and their applications for drug discovery
2012
TASSER‐based refinement of NMR structures
2006
The SWISS-MODEL Repository—new features and functionality
2016
Assessment of protein structure refinement in CASP9
2011
Modeling the assembly order of multimeric heteroprotein complexes
2018
Growth of novel protein structural data
2007 StandoutNobel
Crystal Structures of Protein-Bound Cyclic Peptides
2019
Structure and Nanostructure in Ionic Liquids
2015 Standout
Computer Simulation of Liquids
2017 Standout
The Catalytic Asymmetric Mukaiyama–Michael Reaction of Silyl Ketene Acetals with α,β‐Unsaturated Methyl Esters
2017 StandoutNobel
Toward High-Resolution de Novo Structure Prediction for Small Proteins
2005 StandoutScienceNobel
SWISS-MODEL: homology modelling of protein structures and complexes
2018 Standout
Understanding ethylammonium nitrate stabilized cytochrome c – Molecular dynamics and experimental approach
2014
A Powerful Hydrogen‐Bond‐Donating Organocatalyst for the Enantioselective Intramolecular Oxa‐Michael Reaction of α,β‐Unsaturated Amides and Esters
2013
Molecular Docking and Structure-Based Drug Design Strategies
2015 Standout
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
2012 Standout
Comparative Study of Generalized Born Models: Born Radii and Peptide Folding
2005
Significant Refinement of Protein Structure Models Using a Residue-Specific Force Field
2015
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures
2014 StandoutNobel
ZINC: A Free Tool to Discover Chemistry for Biology
2012 Standout
Catalytic Asymmetric Hydroalkoxylation of C–C Multiple Bonds
2021 StandoutNobel
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase
2008 StandoutNobel
Classification of Intrinsically Disordered Regions and Proteins
2014 Standout
Solvent dramatically affects protein structure refinement
2008 StandoutNobel
Realistic simulation of the activation of voltage-gated ion channels
2012 StandoutNobel
Generalized ensemble methods for de novo structure prediction
2009 StandoutNobel
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
2006
Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles
2012
Macromolecular Modeling with Rosetta
2008 StandoutNobel
Evolutionary-scale prediction of atomic-level protein structure with a language model
2023 StandoutScience
Structure-Function of the G Protein–Coupled Receptor Superfamily
2012
Computational protein structure refinement: almost there, yet still so far to go
2017
Recognition of the HIV Capsid by the TRIM5α Restriction Factor Is Mediated by a Subset of Pre-Existing Conformations of the TRIM5α SPRY Domain
2014
Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F 0 -ATPase
2012 StandoutNobel
Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls
2015
Ligand and Decoy Sets for Docking to G Protein-Coupled Receptors
2011
Assessment of refinement of template‐based models in CASP11
2016
Asymmetric Catalysis via Cyclic, Aliphatic Oxocarbenium Ions
2017 StandoutNobel
Creation of an Amino Acid Network of Structurally Coupled Residues in the Directed Evolution of a Thermostable Enzyme
2009
Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations
2013
Physics‐based protein structure refinement through multiple molecular dynamics trajectories and structure averaging
2013
Effective protein model structure refinement by loop modeling and overall relaxation
2015
Computational Design of Stable and Soluble Biocatalysts
2018
Evolutionary mix-and-match with MFS transporters
2013
Prediction of enzymatic pathways by integrative pathway mapping
2018
Structure-based ligand discovery for the protein–protein interface of chemokine receptor CXCR4
2012
Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases
2009 StandoutNobel
On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes
2010 StandoutNobel
Works of Hao Fan being referenced
Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET
2011
Structure of formylpeptide receptor 2-Gi complex reveals insights into ligand recognition and signaling
2020
Mimicking the action of folding chaperones by Hamiltonian replica‐exchange molecular dynamics simulations: Application in the refinement of de novo models
2012
Refining homology models by combining replica‐exchange molecular dynamics and statistical potentials
2008
Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures
2006
Assignment of Pterin Deaminase Activity to an Enzyme of Unknown Function Guided by Homology Modeling and Docking
2012
Ligand discovery from a dopamine D3 receptor homology model and crystal structure
2011
Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks
2001
Orthosteric and allosteric action of the C5a receptor antagonists
2018
Refinement of homology‐based protein structures by molecular dynamics simulation techniques
2003
ModBase, a database of annotated comparative protein structure models and associated resources
2013
Relative stability of protein structures determined by X‐ray crystallography or NMR spectroscopy: A molecular dynamics simulation study
2003
Structure-based ligand design for flexible proteins: Application of new F-DycoBlock
2001
Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1
2013
Prediction of Substrates for Glutathione Transferases by Covalent Docking
2014
Molecular Docking Screens Using Comparative Models of Proteins
2009
Comparative study of generalized Born models: Protein dynamics
2005
Optimized atomic statistical potentials: assessment of protein interfaces and loops
2013
How Sensitive Are Nanosecond Molecular Dynamics Simulations of Proteins to Changes in the Force Field?
2007
Statistical Potential for Modeling and Ranking of Protein–Ligand Interactions
2011
A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics
2008