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Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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New method for protein secondary structure assignment based on a simple topological descriptor
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Comparing protein–ligand docking programs is difficult
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Bias, reporting, and sharing: computational evaluations of docking methods
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Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?
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Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
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What do we know and when do we know it?
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Community benchmarks for virtual screening
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Recommendations for evaluation of computational methods
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Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide
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Challenges of fragment screening
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Chemical space sampling by different scoring functions and crystal structures
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Virtual ligand screening: strategies, perspectives and limitations
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Reoptimization of MDL Keys for Use in Drug Discovery
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Is There a Difference between Leads and Drugs? A Historical Perspective
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Similarity Searching Using Reduced Graphs
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Further Development of Reduced Graphs for Identifying Bioactive Compounds
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Physics-Based Scoring of Protein−Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening
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SHED: Shannon Entropy Descriptors from Topological Feature Distributions
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Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods
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Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring
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Comparison of Topological, Shape, and Docking Methods in Virtual Screening
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Cross-Docking of Inhibitors into CDK2 Structures. 1
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Investigation of MM-PBSA Rescoring of Docking Poses
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MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization
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How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space
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Comparison of Ligand- and Structure-Based Virtual Screening on the DUD Data Set
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How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information
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Identifying Novel Molecular Structures for Advanced Melanoma by Ligand-Based Virtual Screening
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Comparative Assessment of Scoring Functions on a Diverse Test Set
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Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
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HPPD: Ligand- and Target-Based Virtual Screening on a Herbicide Target
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Similarity Searching in Files of Three-Dimensional Chemical Structures: Analysis of the BIOSTER Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors
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Molecular Dynamics and Free Energy Analyses of Cathepsin D−Inhibitor Interactions: Insight into Structure-Based Ligand Design
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Do Structurally Similar Molecules Have Similar Biological Activity?
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
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A Shape-Based 3-D Scaffold Hopping Method and Its Application to a Bacterial Protein−Protein Interaction
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Validation and Use of the MM-PBSA Approach for Drug Discovery
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A Critical Assessment of Docking Programs and Scoring Functions
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Scaffold Hopping through Virtual Screening Using 2D and 3D Similarity Descriptors: Ranking, Voting, and Consensus Scoring
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Searching Techniques for Databases of Two- and Three-Dimensional Chemical Structures
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Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring
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Benchmarking Sets for Molecular Docking
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Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction Fingerprints
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The RCSB Protein Data Bank: redesigned web site and web services
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Using Extended-Connectivity Fingerprints with Laplacian-Modified Bayesian Analysis in High-Throughput Screening Follow-Up
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Optimal assignment methods for ligand-based virtual screening
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Chemical similarity searches: when is complexity justified?
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Adapting Document Similarity Measures for Ligand-Based Virtual Screening
inferred← citeshttps://doi.org/10.3390/molecules21111554openalex-snapshot
Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors
inferred← citeshttps://doi.org/10.3390/molecules25030665openalex-snapshot
In Silico Strategies in Tuberculosis Drug Discovery
inferred← citeshttps://doi.org/10.3390/molecules26041134openalex-snapshot
Establishing an Analogue Based In Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease
inferred← citeshttps://doi.org/10.3390/molecules28165982openalex-snapshot
Employing Molecular Conformations for Ligand-Based Virtual Screening with Equivariant Graph Neural Network and Deep Multiple Instance Learning
inferred← citeshttps://doi.org/10.3390/molecules28217325openalex-snapshot
Repurposing Drugs for Inhibition against ALDH2 via a 2D/3D Ligand-Based Similarity Search and Molecular Simulation
inferred← citeshttps://doi.org/10.48550/arxiv.1910.14360openalex-snapshot
Prediction of 5-hydroxytryptamine Transporter Inhibitor based on Machine Learning
inferred← citeshttps://doi.org/10.52586/s551openalex-snapshot
Approaches for network based drug discovery
inferred← citeshttps://doi.org/10.52711/0974-360x.2025.00079openalex-snapshot
Search for Lead Compounds and In Vitro Assay of Potential Inhibitors of Plasmodium falciparum Prolyl-tRNA Synthetase from Natural Compound Database
inferred← citeshttps://doi.org/10.7324/japs.2023.123438openalex-snapshot
Machine learning model for antiproliferative virtual screening of herbal compounds against hepatocellular carcinoma
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