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Structural Protein?Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study

https://doi.org/10.1021/ci500319f
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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/prot.20149openalex-snapshot
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
inferredcites →https://doi.org/10.1007/s10822-007-9163-6openalex-snapshot
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?
inferredcites →https://doi.org/10.1021/ci050283kopenalex-snapshot
Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/ci050420dopenalex-snapshot
Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions
inferredcites →https://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
inferredcites →https://doi.org/10.1021/ci200528dopenalex-snapshot
Recognizing Pitfalls in Virtual Screening: A Critical Review
inferredcites →https://doi.org/10.1021/ci600342eopenalex-snapshot
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot
Comparison of Topological, Shape, and Docking Methods in Virtual Screening
inferredcites →https://doi.org/10.1021/ci900043ropenalex-snapshot
APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening
inferredcites →https://doi.org/10.1021/ci900056copenalex-snapshot
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
inferredcites →https://doi.org/10.1021/jm030331xopenalex-snapshot
Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions
inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot
Assessing Scoring Functions for Protein−Ligand Interactions
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/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot
Comparison of Shape-Matching and Docking as Virtual Screening Tools
inferredcites →https://doi.org/10.1021/jm300687eopenalex-snapshot
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
inferredcites →https://doi.org/10.2174/138920306778559395openalex-snapshot
Scoring Functions for Protein-Ligand Docking

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fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions
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An overview of recent advances and challenges in predicting compound-protein interaction (CPI)
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Molecular Docking: From Lock and Key to Combination Lock
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Discovery of Small Molecule and Peptide-based Ligands for the Methyl-Lysine Binding Proteins 53BP1 and PHF1/PHF19
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Novel Natural Inhibitors for Glioblastoma by Targeting Epidermal Growth Factor Receptor and Phosphoinositide 3-kinase
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Targeting WWPI HECT Domain by Small Inhibitors for Restoring PTEN Tumor Suppressive Role in Glioblastoma Therapy
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Advanced in Silico Methods for the Development of Anti- Leishmaniasis and Anti-Trypanosomiasis Agents
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Deep Learning in Drug Target Interaction Prediction: Current and Future Perspectives
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Structure-Based Discovery of Potent Staphylococcus aureus Thymidylate Kinase Inhibitors by Virtual Screening
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Acoplamiento Molecular: Avances Recientes y Retos
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Chemoinformatics and Artificial Intelligence Colloquium: Progress and Challenges to Develop Bioactive Compounds
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Molecular Similarity: Theory, Applications, and Perspectives
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Proteochemometric Models Using Multiple Sequence Alignments and a Subword Segmented Masked Language Model
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Pharmacophore-based Virtual Screening: Identification of Selective Sirtuin 2 Inhibitors
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Neural networks prediction of the protein-ligand binding affinity with circular fingerprints
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Improved Molecular Docking of MAO-B Inhibitors with Glide
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Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review
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Enhancing structure-based virtual screening of MDM2–p53 inhibitors: a benchmark of machine learning vs. traditional docking scoring functions
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Adaptive Learning in AI Agents for the Metaverse: The ALMAA Framework
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Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery
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How Plant Polyhydroxy Flavonoids Can Hinder the Metabolism of Cytochrome 3A4
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Development of a Fingerprint-Based Scoring Function for the Prediction of the Binding Mode of Carbonic Anhydrase II Inhibitors
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Molecular Docking: Shifting Paradigms in Drug Discovery
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Deep Learning in Virtual Screening: Recent Applications and Developments
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Using Machine Learning and Molecular Docking to Leverage Urease Inhibition Data for Virtual Screening
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A PIM-1 Kinase Inhibitor Docking Optimization Study Based on Logistic Regression Models and Interaction Analysis
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Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery
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In silico Identification of Peptide as Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Lung Cancer Treatment
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Protein Ligand Interaction Fingerprints
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Protein Ligand Interaction Fingerprints
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Virtual Screening
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AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery
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Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity
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Enrichment of virtual screening results using induced-fit techniques
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Additional file 1 of Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data
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Large-scale analysis of ligand binding mode similarities in the PDB using interaction fingerprints
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Conception d'un logiciel pour la recherche de nouvelles molécules bioactives
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Identification of new therapeutic targets for cystic fibrosis using systems biology and chemogenomics approaches
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Docking and Machine Learning approaches to explore new scaffolds for molecules of therapeutic interest
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Docking et Deep Learning : affinement de méthodologies in silico pour le développementde stratégies thérapeutiques innovantes
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