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Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening

https://doi.org/10.1021/ci900382e
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What this work says

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

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Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening
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On the Use of Neural Network Ensembles in QSAR and QSPR
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Random Forest: A Classification and Regression Tool for Compound Classification and QSAR Modeling
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Impact of Scoring Functions on Enrichment in Docking-Based Virtual Screening: An Application Study on Renin Inhibitors
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Classifying ‘Drug-likeness' with Kernel-Based Learning Methods
inferredcites →https://doi.org/10.1021/ci049870gopenalex-snapshot
Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design
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Interpreting Computational Neural Network QSAR Models: A Measure of Descriptor Importance
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A Knowledge-Based Weighting Approach to Ligand-Based Virtual Screening
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Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions
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Assessing Different Classification Methods for Virtual Screening
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Virtual Screening of Chinese Herbs with Random Forest
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Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
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Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
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Ligand-Target Interaction-Based Weighting of Substructures for Virtual Screening
inferredcites →https://doi.org/10.1021/ci800466nopenalex-snapshot
Position Specific Interaction Dependent Scoring Technique for Virtual Screening Based on Weighted Protein−Ligand Interaction Fingerprint Profiles
inferredcites →https://doi.org/10.1021/ci900043ropenalex-snapshot
APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening
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Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm020808popenalex-snapshot
DrugScore Meets CoMFA: Adaptation of Fields for Molecular Comparison (AFMoC) or How to Tailor Knowledge-Based Pair-Potentials to a Particular Protein
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/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
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Carbonic Anhydrase Inhibitors. Inhibition of Mitochondrial Isozyme V with Aromatic and Heterocyclic Sulfonamides
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Interaction Profiles of Protein Kinase−Inhibitor Complexes and Their Application to Virtual Screening
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A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/jm050381xopenalex-snapshot
Knowledge-Based Design of Target-Focused Libraries Using Protein−Ligand Interaction Constraints
inferredcites →https://doi.org/10.1021/jm060999mopenalex-snapshot
Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
inferredcites →https://doi.org/10.1021/jm8001058openalex-snapshot
Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction Fingerprints
inferredcites →https://doi.org/10.1021/jm800504qopenalex-snapshot
In SilicoFunctional Profiling of Small Molecules and Its Applications
inferredcites →https://doi.org/10.1021/jm9901475openalex-snapshot
High-Throughput Nuclear Magnetic Resonance-Based Screening
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Random Forests
inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferredcites →https://doi.org/10.1038/nbt1273openalex-snapshot
Structure-based maximal affinity model predicts small-molecule druggability
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Docking and scoring in virtual screening for drug discovery: methods and applications
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Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
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The maximal affinity of ligands
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The Protein Data Bank
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Structural Interaction Fingerprints: A New Approach to Organizing, Mining, Analyzing, and Designing Protein–Small Molecule Complexes
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Neural Networks as Robust Tools in Drug Lead Discovery and Development

What points at this work

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

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Additional file 1 of 2D SIFt: a matrix of ligand-receptor interactions
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