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Inverse Screening @tome server:
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LIST v3 (Large-scale Inverse Screening Tool)
for Protein Kinase
A computational tool to study interactions between protein kinase and small chemicals ligands
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Principle of the study:
This tool tries to dock your ligand into proteins kinase taking into consideration the orientation of the crystallographic ligands (anchors) in the templates and their profile of contacts. Screening is made on a database of suitable homologous complexes supports (models or structures) previously calculated with the pipeline @tome.
Exploration of different docking positions is made by the software Plants that calculates multiple conformations by rotation of dihedral angles or ligand translation. A weight is added if the orientation of the candidate ligand is close to a position of a cristallographic anchor.
For each modeled complex many descriptors are calculated:
- A theoretical affinity (pKd) is calculated using several scoring functions such as MedusaScore, Plants, X-score and DSX.
- Similarity to profile of cristallographics contacts between ligand and receptor in homologous complexes.
- Quality of complex including many descriptors (protein/ligand complementarity, energy, Hbonds, violation...) .
- Theoretical ligand position error (LPE) calculated with a machine learning SVM software including many descriptors.
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