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A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains

https://doi.org/10.1101/776740
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Large-scale comparison of protein sequence alignment algorithms with structure alignments
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An enriched structural kinase database to enable kinome‐wide structure‐based analyses and drug discovery
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The alpha-kinase family: an exceptional branch on the protein kinase tree
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Conserved spatial patterns across the protein kinase family
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The ABC of protein kinase conformations
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The crystal structure of an inactive dimer of PDZ-binding kinase
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Structure of the PAN3 Pseudokinase Reveals the Basis for Interactions with the PAN2 Deadenylase and the GW182 Proteins
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Structural Basis for Auto-Inhibition of the NDR1 Kinase Domain by an Atypically Long Activation Segment
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Recognition of a TG Mismatch
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Overview of manual and automated DNA sequencing by the dideoxy chain termination method
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Crystal Structure of the Atypical Protein Kinase Domain of a TRP Channel with Phosphotransferase Activity
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Calcium/Calmodulin-Dependent Protein Kinase Kinase: Identification of Regulatory Domains
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KLIFS: A Knowledge-Based Structural Database To Navigate Kinase–Ligand Interaction Space
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Crystal Structures of PI3Kα Complexed with PI103 and Its Derivatives: New Directions for Inhibitors Design
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A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase.
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A chemical switch for inhibitor-sensitive alleles of any protein kinase
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Oncogenic kinase signalling
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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
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Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity
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Targeting cancer with small molecule kinase inhibitors
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Kinase mutations in human disease: interpreting genotype–phenotype relationships
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Crystal structure of the Golgi casein kinase
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Defining a new nomenclature for the structures of active and inactive kinases
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Regulatory Mechanism of Ca2+/Calmodulin-dependent Protein Kinase Kinase
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Structure of Pyruvate Dehydrogenase Kinase
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Structural Basis for Autoinhibition and Mutational Activation of Eukaryotic Initiation Factor 2α Protein Kinase GCN2*[boxs]
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A Family Portrait of the RIO Kinases
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Multiple Sequence Alignment Accuracy and Phylogenetic Inference
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Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
inferredcites →https://doi.org/10.1080/15476286.2019.1653679openalex-snapshot
In vitro dimerization of human RIO2 kinase
inferredcites →https://doi.org/10.1093/bioinformatics/btg1086openalex-snapshot
Flexible structure alignment by chaining aligned fragment pairs allowing twists
inferredcites →https://doi.org/10.1093/bioinformatics/btp033openalex-snapshot
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
inferredcites →https://doi.org/10.1093/bioinformatics/btw840openalex-snapshot
Protein multiple sequence alignment benchmarking through secondary structure prediction
inferredcites →https://doi.org/10.1093/database/bar009openalex-snapshot
UniProt Knowledgebase: a hub of integrated protein data
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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
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GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes
inferredcites →https://doi.org/10.1093/nar/gki408openalex-snapshot
The HHpred interactive server for protein homology detection and structure prediction
inferredcites →https://doi.org/10.1093/nar/gku542openalex-snapshot
Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes
inferredcites →https://doi.org/10.1093/nar/gkv155openalex-snapshot
Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex
inferredcites →https://doi.org/10.1093/nar/gkw1033openalex-snapshot
Genenames.org: the HGNC and VGNC resources in 2017
inferredcites →https://doi.org/10.1093/nar/gkw290openalex-snapshot
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
inferredcites →https://doi.org/10.1093/nar/gky916openalex-snapshot
KinaMetrix: a web resource to investigate kinase conformations and inhibitor space
inferredcites →https://doi.org/10.1101/gr.849004openalex-snapshot
WebLogo: A Sequence Logo Generator: Figure 1
inferredcites →https://doi.org/10.1111/gtc.12480openalex-snapshot
3D structural analysis of protein O‐mannosyl kinase, POMK , a causative gene product of dystroglycanopathy
inferredcites →https://doi.org/10.1126/science.1075762openalex-snapshot
The Protein Kinase Complement of the Human Genome
inferredcites →https://doi.org/10.1126/science.3291115openalex-snapshot
The Protein Kinase Family: Conserved Features and Deduced Phylogeny of the Catalytic Domains
inferredcites →https://doi.org/10.1126/scisignal.aaa6711openalex-snapshot
Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases
inferredcites →https://doi.org/10.1126/scisignal.aau8645openalex-snapshot
Illuminating the dark phosphoproteome
inferredcites →https://doi.org/10.1126/scisignal.aav3810openalex-snapshot
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inferredcites →https://doi.org/10.1139/bcb-2013-0015openalex-snapshot
Calmodulin activation of polo-like kinase 1 is required during mitotic entry
inferredcites →https://doi.org/10.1186/1471-2105-10-s1-s4openalex-snapshot
SE: an algorithm for deriving sequence alignment from a pair of superimposed structures
inferredcites →https://doi.org/10.1186/1471-2148-8-95openalex-snapshot
Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
inferredcites →https://doi.org/10.1186/s12859-017-1506-2openalex-snapshot
Classifying kinase conformations using a machine learning approach
inferredcites →https://doi.org/10.1186/s13059-016-1037-6openalex-snapshot
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
inferredcites →https://doi.org/10.1371/journal.pcbi.1003926openalex-snapshot
ECOD: An Evolutionary Classification of Protein Domains
inferredcites →https://doi.org/10.4161/cc.10.14.16494openalex-snapshot
From Plk1 to Plk5
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Structure of PINK1 and mechanisms of Parkinson's disease-associated mutations
inferredcites →https://doi.org/10.7717/peerj.126openalex-snapshot
Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree

What points at this work

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

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A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy
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Protein kinases: Role of their dysregulation in carcinogenesis, identification and inhibition
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The protein common assembly database (ProtCAD)—a comprehensive structural resource of protein complexes
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Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning
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