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Kinases are responsible for phosphorylation of proteins and are involved in many biological processes, including cell signaling. Identifying the kinases that phosphorylate specific phosphoproteins is critical to augment the current understanding of cellular events. Herein, we report a general protocol to study the kinases of a target substrate phosphoprotein using kinase‐catalyzed crosslinking and immunoprecipitation (K‐CLIP). K‐CLIP uses a photocrosslinking γ‐phosphoryl‐modified ATP analog, such as ATP‐arylazide, to covalently crosslink substrates to kinases with UV irradiation. Crosslinked kinase‐substrate complexes can then be enriched by immunoprecipitating the target substrate phosphoprotein, with bound kinase(s) identified using Western blot or mass spectrometry analysis. K‐CLIP is an adaptable chemical tool to investigate and discover kinase‐substrate pairs, which will promote characterization of complex phosphorylation‐mediated cell biology.
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KinDER: A Biocuration Tool for Extracting Kinase Knowledge from Biomedical Literature
Kinases are enzymes that mediate phosphate transfer. Extracting information on kinases from biomedical literature is an important task which has direct implications for applications such as drug design. In this work, we develop KinDER, Kinase Document Extractor and Ranker, a biomedical natural language processing tool for extracting functional and disease related information on kinases. This tool combines information retrieval and machine learning techniques to automatically extract information about protein kinases. First, it uses several bio-ontologies to retrieve documents related to kinases and then uses a supervised classification model to rank them according to their relevance. This was developed to participate in the Text-mining services for Human Kinome Curation Track of the BioCreative VI challenge. According to the official BioCreative evaluation results, KinDER provides stateof- the-art performance for extracting functional information on kinases from abstracts.
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- Award ID(s):
- 1658971
- PAR ID:
- 10046547
- Date Published:
- Journal Name:
- Proceedings of the BioCreative VI Workshop
- Page Range / eLocation ID:
- 51-55
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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