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Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach

Abstract : The ATTRACT protein-protein docking program has been employed to predict protein-protein complex structures in CAPRI rounds 38-45. For 11 out of 16 targets acceptable or better quality solutions have been submitted (~70%). It includes also several cases of peptide-protein docking and the successful prediction of the geometry of carbohydrate-protein interactions. The option of combining rigid body minimization and simultaneous optimization in collective degrees of freedom based on elastic network modes was employed and systematically evaluated. Application to a large benchmark set indicates a modest improvement in docking performance compared to rigid docking. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed.
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Submitted on : Monday, April 19, 2021 - 8:57:22 AM
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Glenn Glashagen, Sjoerd de Vries, Urszula Uciechowska-Kaczmarzyk, Sergey A. Samsonov, Samuel Murail, et al.. Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach. Proteins - Structure, Function and Bioinformatics, Wiley, 2019, 88 (8), pp.1018-1028. ⟨10.1002/prot.25860⟩. ⟨hal-03201555⟩



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