KLIFS: a structural kinase-ligand interaction database.

A.J. Kooistra, G.K. Kanev, O.P.J. van Linden, R. Leurs, I.J.P. de Esch, C. de Graaf

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

Protein kinases play a crucial role in cell signaling and are important drug targets in several therapeutic areas. The KLIFS database contains detailed structural kinase-ligand interaction information derived from all (>2900) structures of catalytic domains of human and mouse protein kinases deposited in the Protein Data Bank in order to provide insights into the structural determinants of kinase-ligand binding and selectivity. The kinase structures have been processed in a consistent manner by systematically analyzing the structural features and molecular interaction fingerprints (IFPs) of a predefined set of 85 binding site residues with bound ligands. KLIFS has been completely rebuilt and extended (>65% more structures) since its first release as a data set, including: novel automated annotation methods for (i) the assessment of ligand-targeted subpockets and the analysis of (ii) DFG and (iii) αC-helix conformations; improved and automated protocols for (iv) the generation of sequence/structure alignments, (v) the curation of ligand atom and bond typing for accurate IFP analysis and (vi) weekly database updates. KLIFS is now accessible via a website (http://klifs.vucompmedchem.nl) that provides a comprehensive visual presentation of different types of chemical, biological and structural chemogenomics data, and allows the user to easily access, compare, search and download the data.
Original languageEnglish
Pages (from-to)D365-D371
JournalNucleic Acids Research
Volume44
Issue numberD1
DOIs
Publication statusPublished - 2016

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Phosphotransferases
Databases
Ligands
Dermatoglyphics
Protein Kinases
Sequence Alignment
Catalytic Domain
Binding Sites
Pharmaceutical Preparations
Proteins
Therapeutics

Cite this

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title = "KLIFS: a structural kinase-ligand interaction database.",
abstract = "Protein kinases play a crucial role in cell signaling and are important drug targets in several therapeutic areas. The KLIFS database contains detailed structural kinase-ligand interaction information derived from all (>2900) structures of catalytic domains of human and mouse protein kinases deposited in the Protein Data Bank in order to provide insights into the structural determinants of kinase-ligand binding and selectivity. The kinase structures have been processed in a consistent manner by systematically analyzing the structural features and molecular interaction fingerprints (IFPs) of a predefined set of 85 binding site residues with bound ligands. KLIFS has been completely rebuilt and extended (>65{\%} more structures) since its first release as a data set, including: novel automated annotation methods for (i) the assessment of ligand-targeted subpockets and the analysis of (ii) DFG and (iii) αC-helix conformations; improved and automated protocols for (iv) the generation of sequence/structure alignments, (v) the curation of ligand atom and bond typing for accurate IFP analysis and (vi) weekly database updates. KLIFS is now accessible via a website (http://klifs.vucompmedchem.nl) that provides a comprehensive visual presentation of different types of chemical, biological and structural chemogenomics data, and allows the user to easily access, compare, search and download the data.",
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KLIFS: a structural kinase-ligand interaction database. / Kooistra, A.J.; Kanev, G.K.; van Linden, O.P.J.; Leurs, R.; de Esch, I.J.P.; de Graaf, C.

In: Nucleic Acids Research, Vol. 44, No. D1, 2016, p. D365-D371.

Research output: Contribution to JournalArticleAcademicpeer-review

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AU - Kanev, G.K.

AU - van Linden, O.P.J.

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AU - de Esch, I.J.P.

AU - de Graaf, C.

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