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@TOME 3.0: Interfacing Protein Structure Modeling and Ligand Docking

2024; Elsevier BV; Volume: 436; Issue: 17 Linguagem: Inglês

10.1016/j.jmb.2024.168704

1089-8638

Jean-Luc Pons, Victor Reys, François Grand, Margarida Viola, Jérôme Gracy, Thomas E. Exner, Gilles Labesse,

Monoclonal and Polyclonal Antibodies Research

Knowledge of protein–ligand complexes is essential for efficient drug design. Virtual docking can bring important information on putative complexes but it is still far from being simultaneously fast and accurate. Receptors are flexible and adapt to the incoming small molecules while docking is highly sensitive to small conformational deviations. Conformation ensemble is providing a mean to simulate protein flexibility. However, modeling multiple protein structures for many targets is seldom connected to ligand screening in an efficient and straightforward manner. @TOME-3 is an updated version of our former pipeline @TOME-2, in which protein structure modeling is now directly interfaced with flexible ligand docking. Sequence-sequence profile comparisons identify suitable PDB templates for structure modeling and ligands from these templates are used to deduce binding sites to be screened. In addition, bound ligand can be used as pharmacophoric restraint during the virtual docking. The latter is performed by PLANTS while the docking poses are analysed through multiple chemoinformatics functions. This unique combination of tools allows rapid and efficient ligand docking on multiple receptor conformations in parallel. @TOME-3 is freely available on the web at https://atome.cbs.cnrs.fr.