KLIFS news updates



31-Oct-2019

Trends in Pharmacological Sciences publication (open access)


04-Sep-2019

Secure browsing with KLIFS


01-Aug-2018

Release version 2.4 - the quality and stability release


30-May-2017

Release version 2.3 - the atypical Protein Kinase (aPK) release


08-Feb-2017

Publication and release 3D-e-Chem-VM


16-Nov-2016

Release version 2.2 - the Virtual Reality release


28-Jul-2016

Release version 2.1 - The KNIME nodes release


24-Oct-2015

Nucleic Acids Research publication


01-Jul-2015

Release version 2.0


13-Aug-2013

Release version 1.0



Trends in Pharmacological Sciences publication (open access)

The enrichment of KLIFS with the structures of atypical kinases in 2017 enabled us to finally compare atypical and eukaryotic protein kinases in a structure-centered manner. For this publication we have investigated their sequences, hydrophobic spines, mutation and SNP hotspots, and inhibitor interaction patterns. This work will hopefully contribute to the design of network medicines: targeting multiple kinases across the barriers of these kinase classes!

Thanks to support from Amsterdam Data Science we could make this work open access. Please contact us if you have any questions or comments!

The article is available here: Trends in Pharmacological Sciences


Secure browsing with KLIFS

It took a while, but our KLIFS server finally has its own SSL certificate. This means that your browser will now mark the connection to KLIFS as secure and will use encryption to communicate with our servers.

Please let us know if you encounter any issues (or have any suggestions) by filling out the contact form.


Release version 2.4 - the quality and stability release

This new release primarily contains new manually curated KLIFS content, updates data links and bugfixes. But that's not all, in order to improve the interactive exploration of the kinase-ligand structures we have included the NGL viewer on the kinase structure detail page in addition to the static images of the structure. As per usual, let us know if you spot any mistakes/issues or have any suggestions.

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Release version 2.3 - the atypical Protein Kinase (aPK) release

With this new release also aPK structures (currently 181 PDBs) have been added to KLIFS after thoroughly refining their reference alignments. All aPK families with a catalytic kinase domain and ePK-like fold (ABC1, PIKK, PI(3)K, and RIO) are now part of KLIFS. The other atypical families (Alpha, Brd, PDHK, and TIF1) are omitted due to the absence of catalytic kinase domains or because they have a non-ePK fold. Please let us know if you spot any mistakes/issues or have any suggestions.

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Publication and release 3D-e-Chem-VM

The 3D-e-Chem team has published its virtual cheminformatics virtual machine in the ACS Journal of Chemical Information and Modeling! This publication also describes the release of the KNIME nodes for the KLIFS database including example workflows using the KLIFS nodes.

Abstract:

3D-e-Chem-VM is an open source, freely available Virtual Machine (https://3d-e-chem.github.io/3D-e-Chem-VM/) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteome-wide databases (e.g. ChEMBLdb and PDB), as well as customized information systems focused on e.g. G Protein-Coupled Receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb).

The article: http://dx.doi.org/10.1021/acs.jcim.6b00686

The virtual machine: https://3d-e-chem.github.io/3D-e-Chem-VM/

The KLIFS knime nodes: https://github.com/3D-e-Chem/knime-klifs/


Release version 2.2 - the Virtual Reality release

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Acknowledgements

We would like to especially thank all KLIFS users that reported issues and/or requested new features. Your input is crucial to maintain a high quality database.


Release version 2.1 - The KNIME nodes release

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Nucleic Acids Research publication

Nucleic Acids Research has accepted our manuscript regarding the new KLIFS database and website for publication in the database 2016 issue. You can freely access the article: doi: 10.1093/nar/gkv1082.


Release version 2.0

The second version of KLIFS as described in the Nucleic Acids Research paper (doi: 10.1093/nar/gkv1082). KLIFS is now accessible at http://klifs.vu-compmedchem.nl and has many added features.

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Release version 1.0

The initial version of KLIFS as used for the ACS Journal of Medicinal Chemistry publication (doi: 10.1021/jm400378w). It contains the analysis of 1734 PDB structures covering 190 different human kinases.

KLIFS v1.0 is available as a dataset at Zenodo:

DOI