KinomeRun: An interactive utility for kinome target screening and interaction fingerprint analysis towards holistic visualization on kinome tree
- 16 May 2020
- journal article
- research article
- Published by Wiley in Chemical Biology & Drug Design
- Vol. 96 (4), 1162-1175
- https://doi.org/10.1111/cbdd.13705
Abstract
Kinases are key targets for many of the pathological conditions. Inverse screening of ligands serves as an essential mode to identify potential kinase targets in modern drug discovery research. Hence, we intend to develop KinomeRun, a robust pipeline for inverse screening and kinome tree visualization through the seamless integration of kinome structures, docking and kinome‐drug interaction fingerprint analysis. In this pipeline, the hurdle of residue numbering in kinome is also resolved by creating a common index file with the conserved kinase pocket residues for comparative interaction analysis. KinomeRun can be used to screen the ligands of interest docked against multiple kinase structures in parallel around the kinase binding site and also to filter out the targets with unique interaction patterns. This automation is essential for prioritization of kinase targets that show specificity for a given drug and will also serve as a crucial tool kit for holistic approaches in kinase drug discovery. KinomeRun is developed using python and bash programming language and is distributed freely under the GNU GPL license‐3.0 and can be downloaded at https://github.com/inpacdb/KinomeRun. The tutorial videos for installation, target screening and customized filteration are available at https://www.youtube.com/playlist?list=PLuIaEFtMVgQ7v__WigQH9ilGVxrfI1LKs and also be downloaded for offline viewing from the github link.Keywords
Funding Information
- Department of Biotechnology, Ministry of Science and Technology, India (DBT/2015/VRF/363)
This publication has 61 references indexed in Scilit:
- Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome treePeerJ, 2013
- idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approachNucleic Acids Research, 2012
- Open Babel: An open chemical toolboxJournal of Cheminformatics, 2011
- Lck is a key target of imatinib and dasatinib in T-cell activationLeukemia, 2010
- AP24534, a Pan-BCR-ABL Inhibitor for Chronic Myeloid Leukemia, Potently Inhibits the T315I Mutant and Overcomes Mutation-Based ResistanceCancer Cell, 2009
- Myelosuppression and kinase selectivity of multikinase angiogenesis inhibitorsBritish Journal of Cancer, 2009
- AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreadingJournal of Computational Chemistry, 2009
- Inhibition of Src Family Kinases with Dasatinib Blocks Migration and Invasion of Human Melanoma CellsMolecular Cancer Research, 2008
- The Btk tyrosine kinase is a major target of the Bcr-Abl inhibitor dasatinibProceedings of the National Academy of Sciences, 2007
- TarFisDock: a web server for identifying drug targets with docking approachNucleic Acids Research, 2006