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Improving Virtual Screening Performance against Conformational Variations of Receptors by Shape Matching with Ligand Binding Pocket

https://doi.org/10.1021/ci9002365
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Effective energy function for proteins in solution
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Current topics in computer‐aided drug design
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Improved protein–ligand docking using GOLD
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Comparative Protein Modelling by Satisfaction of Spatial Restraints
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Binding site characteristics in structure-based virtual screening: evaluation of current docking tools
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Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
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Virtual ligand screening: strategies, perspectives and limitations
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Managing protein flexibility in docking and its applications
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High-throughput docking for lead generation
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A Comparison of Field-Based Similarity Searching Methods: CatShape, FBSS, and ROCS
inferredcites →https://doi.org/10.1021/ci700368popenalex-snapshot
Novel Approach to Structure-Based Pharmacophore Search Using Computational Geometry and Shape Matching Techniques
inferredcites →https://doi.org/10.1021/ci800324mopenalex-snapshot
Identifying and Characterizing Binding Sites and Assessing Druggability
inferredcites →https://doi.org/10.1021/ci8004226openalex-snapshot
How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
inferredcites →https://doi.org/10.1021/jm0300330openalex-snapshot
Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes
inferredcites →https://doi.org/10.1021/jm030209yopenalex-snapshot
Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm049092jopenalex-snapshot
Virtual Screening Workflow Development Guided by the “Receiver Operating Characteristic” Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4
inferredcites →https://doi.org/10.1021/jm050639jopenalex-snapshot
Novel Human Lipoxygenase Inhibitors Discovered Using Virtual Screening with Homology Models
inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot
Comparison of Shape-Matching and Docking as Virtual Screening Tools
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm701157gopenalex-snapshot
Discovery of Novel Cdc25 Phosphatase Inhibitors with Micromolar Activity Based on the Structure-Based Virtual Screening
inferredcites →https://doi.org/10.1023/a:1008015827877openalex-snapshot
The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1073/pnas.44.2.98openalex-snapshot
Application of a Theory of Enzyme Specificity to Protein Synthesis
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/protein/12.9.713openalex-snapshot
Folding funnels and binding mechanisms
inferredcites →https://doi.org/10.1126/science.1749933openalex-snapshot
The Energy Landscapes and Motions of Proteins
inferredcites →https://doi.org/10.2174/1386207043328706openalex-snapshot
Virtual Screening Methods that Complement HTS

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Stalis: A Computational Method for Template‐Based Ab Initio Ligand Design
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Predicting Cyclooxygenase Inhibition by Three‐Dimensional Pharmacophoric Profiling. Part I: Model Generation, Validation and Applicability in Ethnopharmacology
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BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures
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Application of QSAR and Shape Pharmacophore Modeling Approaches for Targeted Chemical Library Design
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Exploring the Significance of Experimental and Computational Methods in Protein Structure Determination
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Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00561openalex-snapshot
CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement
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CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00895openalex-snapshot
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00416openalex-snapshot
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes
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Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein–Protein Interactions
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DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites
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Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site
inferred← citeshttps://doi.org/10.1021/ci100263popenalex-snapshot
Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods
inferred← citeshttps://doi.org/10.1021/ci1004527openalex-snapshot
Comparison of Virtual High-Throughput Screening Methods for the Identification of Phosphodiesterase-5 Inhibitors
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Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors
inferred← citeshttps://doi.org/10.1021/ci3002638openalex-snapshot
Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations
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Shape-Based Reprofiling of FDA-Approved Drugs for the H1 Histamine Receptor
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DiffBindFR: an SE(3) equivariant network for flexible protein–ligand docking
inferred← citeshttps://doi.org/10.1073/pnas.2511925122openalex-snapshot
Flexible protein–ligand docking with diffusion-based side-chain packing
inferred← citeshttps://doi.org/10.1074/jbc.m112.352385openalex-snapshot
Biophysical and Structural Characterization of a Sequence-diverse Set of Solute-binding Proteins for Aromatic Compounds
inferred← citeshttps://doi.org/10.1080/17460441.2025.2458666openalex-snapshot
Virtual screening: hope, hype, and the fine line in between
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Assessment of AlphaFold structures and optimization methods for virtual screening
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PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking
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Building shape-focused pharmacophore models for effective docking screening
inferred← citeshttps://doi.org/10.1371/journal.pone.0059315openalex-snapshot
Identification, Design and Bio-Evaluation of Novel Hsp90 Inhibitors by Ligand-Based Virtual Screening
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PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking
inferred← citeshttps://doi.org/10.21203/rs.3.rs-5429173/v1openalex-snapshot
PackDock is a Flexible Protein-Ligand Docking Approach with Diffusion-Based Side Chain Packing
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Molecular Shape Technologies in Drug Discovery: Methods and Applications
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De-Novo Design of Hits Against New Delhi Metallo-β-Lactamase Enzyme
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Peptides Binding Cocaine: A Strategy to Design Biomimetic Receptors
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