1. KinMap: a web-based tool for interactive navigation through human kinome data
- Author
-
Simone Fulle, Sameh Eid, Friedrich Rippmann, Andrea Volkamer, and Samo Turk
- Subjects
Models, Molecular ,0301 basic medicine ,Scheme (programming language) ,Biology ,Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Protein kinases ,Structural Biology ,Carcinoma, Non-Small-Cell Lung ,Interactive annotation ,Humans ,Web application ,Kinome ,Human kinome tree ,Databases, Protein ,Protein Kinase Inhibitors ,Molecular Biology ,Phylogeny ,computer.programming_language ,Internet ,Class (computer programming) ,Information retrieval ,business.industry ,Applied Mathematics ,Molecular Sequence Annotation ,computer.file_format ,chEMBL ,Protein Data Bank ,Data science ,Computer Science Applications ,Tree (data structure) ,030104 developmental biology ,Drug Design ,030220 oncology & carcinogenesis ,Images ,The Internet ,business ,computer ,Software - Abstract
Background Annotations of the phylogenetic tree of the human kinome is an intuitive way to visualize compound profiling data, structural features of kinases or functional relationships within this important class of proteins. The increasing volume and complexity of kinase-related data underlines the need for a tool that enables complex queries pertaining to kinase disease involvement and potential therapeutic uses of kinase inhibitors. Results Here, we present KinMap, a user-friendly online tool that facilitates the interactive navigation through kinase knowledge by linking biochemical, structural, and disease association data to the human kinome tree. To this end, preprocessed data from freely-available sources, such as ChEMBL, the Protein Data Bank, and the Center for Therapeutic Target Validation platform are integrated into KinMap and can easily be complemented by proprietary data. The value of KinMap will be exemplarily demonstrated for uncovering new therapeutic indications of known kinase inhibitors and for prioritizing kinases for drug development efforts. Conclusion KinMap represents a new generation of kinome tree viewers which facilitates interactive exploration of the human kinome. KinMap enables generation of high-quality annotated images of the human kinome tree as well as exchange of kinome-related data in scientific communications. Furthermore, KinMap supports multiple input and output formats and recognizes alternative kinase names and links them to a unified naming scheme, which makes it a useful tool across different disciplines and applications. A web-service of KinMap is freely available at http://www.kinhub.org/kinmap/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1433-7) contains supplementary material, which is available to authorized users.
- Published
- 2017