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Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE against JNK-3 and β-Secretase
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/jcc.540150503openalex-snapshot
ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot
A Fast Flexible Docking Method using an Incremental Construction Algorithm
inferredcites →https://doi.org/10.1006/jmbi.2001.4551openalex-snapshot
FlexE: efficient molecular docking considering protein structure variations
inferredcites →https://doi.org/10.1016/0022-2836(91)90859-5openalex-snapshot
“Soft docking”: Matching of molecular surface cubes
inferredcites →https://doi.org/10.1016/j.jmb.2004.08.018openalex-snapshot
Apo and Inhibitor Complex Structures of BACE (β-secretase)
inferredcites →https://doi.org/10.1016/s0022-2836(05)80038-5openalex-snapshot
Ligand docking to proteins with discrete side-chain flexibility
inferredcites →https://doi.org/10.1016/s1074-5521(03)00159-5openalex-snapshot
The Structure of JNK3 in Complex with Small Molecule Inhibitors
inferredcites →https://doi.org/10.1021/bi026232nopenalex-snapshot
Crystal Structure of Memapsin 2 (β-Secretase) in Complex with an Inhibitor OM00-3
inferredcites →https://doi.org/10.1021/bi048106kopenalex-snapshot
Structural Locations and Functional Roles of New Subsites S5, S6, and S7 in Memapsin 2 (β-Secretase),
inferredcites →https://doi.org/10.1021/ci034289qopenalex-snapshot
Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment
inferredcites →https://doi.org/10.1021/jm049388popenalex-snapshot
Identification of a Small Molecule Nonpeptide Active Site β-Secretase Inhibitor That Displays a Nontraditional Binding Mode for Aspartyl Proteases
inferredcites →https://doi.org/10.1023/a:1016399411208openalex-snapshot
Flexible docking under pharmacophore type constraints
inferredcites →https://doi.org/10.1038/nrd1129openalex-snapshot
Implications of protein flexibility for drug discovery
inferredcites →https://doi.org/10.1096/fasebj.11.2.9039959openalex-snapshot
Computation of the binding of fully flexible peptides to proteins with flexible side chains
inferredcites →https://doi.org/10.1126/science.290.5489.150openalex-snapshot
Structure of the Protease Domain of Memapsin 2 (β-Secretase) Complexed with Inhibitor
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Structure‐Based Design of BACE Inhibitors: Technical and Practical Aspects of Preparation, 3‐Dimensional Structure, and Computational Analysis
inferred← citeshttps://doi.org/10.1002/cbic.202100570openalex-snapshot
NMR Data‐Driven Docking of HDM2‐Inhibitor Complexes
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Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE Against JNK‐3 and β‐Secretase.
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Ensemble-docking approach on BACE-1: Pharmacophore Perception and Directives for Drug Development
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Structure and modeling in the design of β‐ and γ‐secretase inhibitors
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Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility
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Flexible protein‐ligand docking using the Fleksy protocol
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Modeling loop backbone flexibility in receptor‐ligand docking simulations
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EDock‐ML: A web server for using ensemble docking with machine learning to aid drug discovery
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Docking and scoring with alternative side‐chain conformations
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Receptor flexibility in small‐molecule docking calculations
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(How to) Profit from Molecular Dynamics-based Ensemble Docking
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Applications of Computer-Aided Drug Design
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How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis
inferred← citeshttps://doi.org/10.1007/s10822-008-9182-yopenalex-snapshot
Improving database enrichment through ensemble docking
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Alzheimer's disease drug development based on Computer-Aided Drug Design
inferred← citeshttps://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot
Flexible ligand docking to multiple receptor conformations: a practical alternative
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00169openalex-snapshot
A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00010openalex-snapshot
Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking
inferred← citeshttps://doi.org/10.1021/ci2001742openalex-snapshot
Accurate Prediction of the Bound Form of the Akt Pleckstrin Homology Domain Using Normal Mode Analysis To Explore Structural Flexibility
inferred← citeshttps://doi.org/10.1021/ci200366zopenalex-snapshot
Combining Dyad Protonation and Active Site Plasticity in BACE-1 Structure-Based Drug Design
inferred← citeshttps://doi.org/10.1021/ci400620fopenalex-snapshot
Screen3D: A Novel Fully Flexible High-Throughput Shape-Similarity Search Method
inferred← citeshttps://doi.org/10.1021/ci700223popenalex-snapshot
Impact of Ligand Protonation on Virtual Screening against β-Secretase (BACE1)
inferred← citeshttps://doi.org/10.1021/ci8003732openalex-snapshot
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes
inferred← citeshttps://doi.org/10.1021/ci9003078openalex-snapshot
Scoring Ensembles of Docked Protein:Ligand Interactions for Virtual Lead Optimization
inferred← citeshttps://doi.org/10.1021/cr300314qopenalex-snapshot
Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity
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A Flexible Approach to Induced Fit Docking
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siRNA screen identifies QPCT as a druggable target for Huntington's disease
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Prospecting for new catechol- O -methyltransferase (COMT) inhibitors as a potential treatment for Parkinson’s disease: a study by molecular dynamics and structure-based virtual screening
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FlexE ensemble docking approach to virtual screening for CDK2 inhibitors
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Loopholes and missing links in protein modeling
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Tubulin Inhibitor Identification by Bioactive Conformation Alignment Pharmacophore‐Guided Virtual Screening
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Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE)
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Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening
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Application of Consensus Scoring and Principal Component Analysis for Virtual Screening against β-Secretase (BACE-1)
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Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments
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Structure-guided design of β-secretase (BACE-1) inhibitors
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Flexible receptor docking for drug discovery
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Receptor Flexibility in Ligand Docking and Virtual Screening
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Cognitive Enhancers (Nootropics). Part 2: Drugs Interacting with Enzymes
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Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement
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Targeting the C-Terminal Domain Small Phosphatase 1
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Development of new virtual screening methods and novel unbiased benchmarking data sets
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