ArticleNucleic acids research2022
Kincore: a web resource for structural classification of protein kinases and their inhibitors.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed, 108 citations in OpenAlex.
- Predicting Oncogenic Mutants of Epidermal Growth Factor Receptor in Lung Cancer by Molecular Dynamics Simulation with Machine Learning.ACS omega · 2026Article
- A curated benchmark for cofolding models on kinase conformational states.npj drug discovery · 2026Article
- Explainable AI reveals the allosteric blind spot in protein-ligand binding predictions.Cell reports. Physical science · 2026Article
- Decoding the allosteric grammar of protein kinases: A dual-stream framework integrating protein language models and energy landscape frustration analysis.Protein science : a publication of the Protein Society · 2026Article
- Integrated Framework for Probing Multimodal Protein Foundation Models with Structure-Functional Interpretability Analysis in Detection of Allosteric Binding Sites.bioRxiv : the preprint server for biology · 2026Article
- KASSPer: kinase active site structure prediction using protein and ligand language models and its application to virtual screening.Bioinformatics (Oxford, England) · 2026Article
- Revisiting Target-Aware de novo Molecular Generation with TarPass: Between Rational Design and Texas Sharpshooter.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Tyrosine kinases sample unique activation ensembles.bioRxiv : the preprint server for biology · 2026Article
- Predicting and Decoding Allosteric Binding Sites Using Protein Language Models and Structure-Based Machine Learning: An Energy Landscape-Guided Explainable AI Framework.Journal of chemical theory and computation · 2026Article
- A PKA-selective inhibitor captures an open but more ordered conformation of the PKA catalytic subunit.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Evaluating generalization in protein-ligand cofolding methods.Nature structural & molecular biology · 2026Article
- Results of a Large-Scale Study of the Binding of 50 Type II Inhibitors to 348 Kinases: The Role of Protein Reorganization.Journal of medicinal chemistry · 2026Article
- KinConfBench: A Curated Benchmark for Cofolding Models on Kinase Conformational States.bioRxiv : the preprint server for biology · 2026Article
- Mechanism of MEK1 activation by phosphorylation.Biophysical journal · 2026Article
- Fine-Tuning DiffDock-L for Allosteric Kinase Docking.Journal of chemical information and modeling · 2026Article
- Novel universal domain-centric method for protein classification.Scientific reports · 2026Article
- Natural Product-like Fragments Unlock Novel Chemotypes for a Kinase Target─Exploring Options beyond the Flatland.Journal of chemical information and modeling · 2026Article
- Defining the Active Conformation of Typical Protein Kinase Domains from Substrate-Bound PDB Structures Enables Active-State AlphaFold2 Models for All 437 Human Catalytic Protein Kinases.bioRxiv : the preprint server for biology · 2026Article
- Results of a large scale study of the binding of 50 type II inhibitors to 348 kinases: The role of protein reorganization.bioRxiv : the preprint server for biology · 2026Article
- Markovian state models uncover casein kinase 1 dynamics that govern circadian period.Biophysical journal · 2025Article
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2 authors at 1 institution in 1 country.
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Abstract
The active form of kinases is shared across different family members, as are several commonly observed inactive forms. We previously performed a clustering of the conformation of the activation loop of all protein kinase structures in the Protein Data Bank (PDB) into eight classes based on the dihedral angles that place the Phe side chain of the DFG motif at the N-terminus of the activation loop. Our clusters are strongly associated with the placement of the activation loop, the C-helix, and other structural elements of kinases. We present Kincore, a web resource providing access to our conformational assignments for kinase structures in the PDB. While other available databases provide conformational states or drug type but not both, KinCore includes the conformational state and the inhibitor type (Type 1, 1.5, 2, 3, allosteric) for each kinase chain. The user can query and browse the database using these attributes or determine the conformational labels of a kinase structure using the web server or a standalone program. The database and labeled structure files can be downloaded from the server. Kincore will help in understanding the conformational dynamics of these proteins and guide development of inhibitors targeting specific states. Kincore is available at http://dunbrack.fccc.edu/kincore.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.