KinMap: a web-based tool for interactive navigation through human kinome data

Abstract

BackgroundAnnotations 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.ResultsHere, 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.ConclusionKinMap 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 materialThe online version of this article (doi:10.1186/s12859-016-1433-7) contains supplementary material, which is available to authorized users.

Coral: Clear and Customizable Visualization of Human Kinome Data

“…These figures are powerful tools for data interpretation and communication but are labor intensive to create and often infeasible for large or more complex experimental data sets. To address this issue, several programs have been developed to automate kinome visualization including Kinome Render (Chartier et al, 2013), the NCGC Kinome Viewer (tripod.nih.gov), and KinMap (Eid et al, 2017), which have been widely adopted by the kinase research community. Because these existing methods encode information solely by adding nodes to the existing image created by Cell Signaling Technology, they suffer from three limitations: (1) they offer no ability to recolor kinase branches either for aesthetic purposes or to encode information, (2) they only feature a single paradigm for kinome representation, the semi-quantitative tree, and (3) they produce low-resolution images that are not well suited for publication.…”

Probing 2H‐Indazoles as Templates for SGK1, Tie2, and SRC Kinase Inhibitors

“…The size of dots refers to measured percent inhibition. Illustration created using http://kinhub.org/kinmap/ webservice and reproduced courtesy of Cell Signaling Technology, Inc.…”

Identification of NEK3 and MOK as novel targets for lithium

“…A total of 413 protein sequences of kinase catalytic domains from the human kinome were downloaded from KinBase (Eid, Turk, Volkamer, Rippmann, & Fulle, 2017). Kalign (Lassmann & Sonnhammer, 2005) was used for sequence alignment and GSK3β was used as the reference kinase.…”