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Enhancing the Accuracy of Chemogenomic Models with a Three-Dimensional Binding Site Kernel

https://doi.org/10.1021/ci200166t

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What this work says

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

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Towards Proteome–Wide Interaction Models Using the Proteochemometrics Approach

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Best Practices for QSAR Model Development, Validation, and Exploitation

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Database Systems for Knowledge-Based Discovery

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ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI)

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Virtual Screen for Ligands of Orphan G Protein-Coupled Receptors

inferredcites →https://doi.org/10.1021/ci050372xopenalex-snapshot

sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank

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The Pharmacophore Kernel for Virtual Screening with Support Vector Machines

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Extended-Connectivity Fingerprints

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Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space

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Development and Validation of a Novel Protein−Ligand Fingerprint To Mine Chemogenomic Space: Application to G Protein-Coupled Receptors and Their Ligands

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Ligand Prediction from Protein Sequence and Small Molecule Information Using Support Vector Machines and Fingerprint Descriptors

inferredcites →https://doi.org/10.1021/ci900182qopenalex-snapshot

Multi-Assay-Based Structure−Activity Relationship Models: Improving Structure−Activity Relationship Models by Incorporating Activity Information from Related Targets

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Ligand Prediction for Orphan Targets Using Support Vector Machines and Various Target-Ligand Kernels Is Dominated by Nearest Neighbor Effects

inferredcites →https://doi.org/10.1021/ci900349yopenalex-snapshot

Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites

inferredcites →https://doi.org/10.1021/ci960463hopenalex-snapshot

Rapid Quantification of Molecular Diversity for Selective Database Acquisition

inferredcites →https://doi.org/10.1021/jm030580lopenalex-snapshot

The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures

inferredcites →https://doi.org/10.1038/nbt1284openalex-snapshot

Relating protein pharmacology by ligand chemistry

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Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia

inferredcites →https://doi.org/10.1038/sj.bjp.0707307openalex-snapshot

Chemogenomic approaches to rational drug design

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Chemogenomic approaches to drug discovery: similar receptors bind similar ligands

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Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures

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Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets

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The Protein Data Bank

inferredcites →https://doi.org/10.1093/nar/gkj039openalex-snapshot

AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB

inferredcites →https://doi.org/10.1093/nar/gkl999openalex-snapshot

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

inferredcites →https://doi.org/10.1093/nar/gkm958openalex-snapshot

DrugBank: a knowledgebase for drugs, drug actions and drug targets

inferredcites →https://doi.org/10.1093/nar/gkp456openalex-snapshot

PubChem: a public information system for analyzing bioactivities of small molecules

inferredcites →https://doi.org/10.1093/nar/gkp846openalex-snapshot

The Universal Protein Resource (UniProt) in 2010

inferredcites →https://doi.org/10.1093/nar/gkp937openalex-snapshot

STITCH 2: an interaction network database for small molecules and proteins

inferredcites →https://doi.org/10.1186/1471-2105-11-339openalex-snapshot

Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques

inferredcites →https://doi.org/10.1186/1471-2105-9-363openalex-snapshot

Virtual screening of GPCRs: An in silico chemogenomics approach

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PocketMatch: A new algorithm to compare binding sites in protein structures

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Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening

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Machine Learning for In Silico Virtual Screening and Chemical Genomics: New Strategies

What points at this work

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

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Protein Structural Databases in Drug Discovery

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Molecular Interaction Fingerprints

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Progress in the Visualization and Mining of Chemical and Target Spaces

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Statistical Profiling of One Promiscuous Protein Binding Site: Illustrated by Urokinase Catalytic Domain

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Computational Profiling of Bioactive Compounds Using a Target-Dependent Composite Workflow

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Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects

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