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2 results for “KLIFS”
KLIFS: A Knowledge-Based Structural Database To Navigate Kinase–Ligand Interaction Space
<p>The Kinase-Ligand Interaction Fingerprints and Structure database (KLIFS) contains a consistent structural alignment and deconstruction of the kinase domains from over 1734 PDB structures covering 190 different human kinases. </p> <p>Every crystal structure was structurally aligned in a consistent manner, subsequently broken down from the full complex into separate structural parts: the protein, the orthosteric ligand-binding pocket (85 aligned residues covering the catalytic cleft), orthosteric and allosteric ligand(s), ions, organometallics, cofactors, and waters. By combining the pocket with the orthosteric ligand all interactions are annotated using Interactions FingerPrints (IFPs) for systematic comparison.</p>
Example workflow using KLIFS nodes in KNIME - identifying structures with similar molecules
<p>This is KNIME workflow created during the recording of the following <a href="https://www.youtube.com/channel/UCzSo1G_wyTv1vp42AhFDT8A">YouTube demonstration video</a>.</p> <p>Using this workflow, the user can draw a molecule and compare this molecule to all ligands from the KLIFS database (<a href="https://klifs.net">https://klifs.net</a>) to identify structures with molecules that are similar to the drawn molecule.</p> <p>In this workflow the follow steps are performed:</p> <ul> <li>Draw a molecule</li> <li>Collect all kinase ligands with a known structures from KLIFS</li> <li>Compare all KLIFS ligands to the drawn molecule using the ECFP-4 fingerprint and calculate a Tanimoto score </li> <li>Select the highest scoring three ligands and search for their PDB structures</li> <li>Collect the MOL2 files of the ligands as observed while binding in the PDB structures (note: all the PDB structures were first aligned by KLIFS)</li> </ul>
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