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Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach

https://doi.org/10.1021/mp1002976
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What this work says

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

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Editorial: Drug Discovery Process for Kinease Inhibitors
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Kinomics—structural biology and chemogenomics of kinase inhibitors and targets
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Doing more than just the structure—structural genomics in kinase drug discovery
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A General Strategy for Creating “Inactive-Conformation” Abl Inhibitors
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A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction
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Comparative modeling for protein structure prediction
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Sequence and Structure Classification of Kinases
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ROC with confidence — a Perl program for receiver operator characteristic curves
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The Structure of JNK3 in Complex with Small Molecule Inhibitors
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Structure-activity relationship homology (SARAH): a conceptual framework for drug discovery in the genomic era
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Kinomics: characterizing the therapeutically validated kinase space
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The development and therapeutic potential of protein kinase inhibitors
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ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
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Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening
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Protein−Ligand Docking against Non-Native Protein Conformers
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Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family
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QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data Sets
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Chemical Similarity Searching
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Structural Classification of Protein Kinases Using 3D Molecular Interaction Field Analysis of Their Ligand Binding Sites: Target Family Landscapes
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Novel 2-Aminopyrimidine Carbamates as Potent and Orally Active Inhibitors of Lck: Synthesis, SAR, and in Vivo Antiinflammatory Activity
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Molecular Recognition of Protein Kinase Binding Pockets for Design of Potent and Selective Kinase Inhibitors
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Assessment of Chemical Coverage of Kinome Space and Its Implications for Kinase Drug Discovery
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Selectively Nonselective Kinase Inhibition: Striking the Right Balance
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Computational Modeling of Kinase Inhibitor Selectivity
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In Silico Drug Profiling of the Human Kinome Based on a Molecular Marker for Cross Reactivity
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Oncogenic kinase signalling
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A small molecule–kinase interaction map for clinical kinase inhibitors
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A quantitative analysis of kinase inhibitor selectivity
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Hit and lead generation: beyond high-throughput screening
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Rho kinase, a promising drug target for neurological disorders
inferredcites →https://doi.org/10.1042/0264-6021:3510095openalex-snapshot
Specificity and mechanism of action of some commonly used protein kinase inhibitors
inferredcites →https://doi.org/10.1042/bj3510095openalex-snapshot
Specificity and mechanism of action of some commonly used protein kinase inhibitors
inferredcites →https://doi.org/10.1042/bst0350007openalex-snapshot
Protein kinases and their therapeutic exploitation
inferredcites →https://doi.org/10.1073/pnas.0707684105openalex-snapshot
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
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An Easily Implemented Generalised Inverse Gaussian Generator
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Matrix2png: a utility for visualizing matrix data
inferredcites →https://doi.org/10.1093/biomet/30.1-2.81openalex-snapshot
A NEW MEASURE OF RANK CORRELATION
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/gki524openalex-snapshot
TM-align: a protein structure alignment algorithm based on the TM-score
inferredcites →https://doi.org/10.1096/fasebj.9.8.7768349openalex-snapshot
The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification 1
inferredcites →https://doi.org/10.1097/tp.0b013e318166acc4openalex-snapshot
Novel Immunosuppression
inferredcites →https://doi.org/10.1126/science.1075762openalex-snapshot
The Protein Kinase Complement of the Human Genome
inferredcites →https://doi.org/10.1126/science.1095920openalex-snapshot
Protein Kinase Inhibitors: Insights into Drug Design from Structure
inferredcites →https://doi.org/10.1186/1471-2105-9-543openalex-snapshot
PocketMatch: A new algorithm to compare binding sites in protein structures
inferredcites →https://doi.org/10.1186/1472-6807-8-2openalex-snapshot
Preservation of protein clefts in comparative models
inferredcites →https://doi.org/10.1200/jco.2010.28.15_suppl.e13665openalex-snapshot
ACTB-1003: An oral kinase inhibitor targeting cancer mutations (FGFR), angiogenesis (VEGFR2, TEK), and induction of apoptosis (RSK and p70S6K).
inferredcites →https://doi.org/10.1358/dof.2006.031.06.997160openalex-snapshot
PKC - A target for treating diabetic complications
inferredcites →https://doi.org/10.1371/journal.pcbi.1000405openalex-snapshot
FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling
inferredcites →https://doi.org/10.1371/journal.pgen.0020042openalex-snapshot
PRKCA and Multiple Sclerosis: Association in Two Independent Populations
inferredcites →https://doi.org/10.1517/17460441.2010.504203openalex-snapshot
Targeting kinases for the treatment of inflammatory diseases
inferredcites →https://doi.org/10.1529/biophysj.104.045385openalex-snapshot
Tertiary Structure Predictions on a Comprehensive Benchmark of Medium to Large Size Proteins
inferredcites →https://doi.org/10.21236/ada439508openalex-snapshot
CLUTO - A Clustering Toolkit
inferredcites →https://doi.org/10.2174/092986708783503212openalex-snapshot
From Single- to Multi-Target Drugs in Cancer Therapy: When Aspecificity Becomes an Advantage
inferredcites →https://doi.org/10.2174/1381612043452695openalex-snapshot
High-Throughput Structural Biology in Drug Discovery: Protein Kinases
inferredcites →https://doi.org/10.2174/1381612053764850openalex-snapshot
Strategies for the Design of Potent and Selective Kinase Inhibitors
inferredcites →https://doi.org/10.2174/138955708786141043openalex-snapshot
Strategies for the Design of Selective Protein Kinase Inhibitors
inferredcites →https://doi.org/10.2174/187152910793743869openalex-snapshot
Protein Kinase C – Possible Therapeutic Target to Treat Cardiovascular Diseases
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R: A Language and Environment for Statistical Computing

What points at this work

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

inferred← citeshttps://doi.org/10.1002/minf.201300082openalex-snapshot
Identification of Similar Binding Sites to Detect Distant Polypharmacology
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Local Alignment of Ligand Binding Sites in Proteins for Polypharmacology and Drug Repositioning
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Computational Modelling of Kinase Inhibitors as Anti-Alzheimer Agents
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In Silico Drug–Target Profiling
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Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development
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Structure-based systems biology for analyzing off-target binding
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Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
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Kinase-Kernel Models: Accurate In silico Screening of 4 Million Compounds Across the Entire Human Kinome
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FINDSITE comb : A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach
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A New Target for an Old Drug: Identifying Mitoxantrone as a Nanomolar Inhibitor of PIM1 Kinase via Kinome-Wide Selectivity Modeling
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FINDSITEX: A Structure-Based, Small Molecule Virtual Screening Approach with Application to All Identified Human GPCRs
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GraphGR: A graph neural network to predict the effect of pharmacotherapy on the cancer cell growth
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Integration of Biodynamic Imaging and RNA-seq classifies chemotherapy response in canine diffuse large B-cell lymphoma
inferred← citeshttps://doi.org/10.1186/s12885-022-10293-0openalex-snapshot
Artificial intelligence to guide precision anticancer therapy with multitargeted kinase inhibitors
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003829openalex-snapshot
eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models
inferred← citeshttps://doi.org/10.3389/fgene.2014.00196openalex-snapshot
Computational methods for analysis and inference of kinase/inhibitor relationships
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