Journal of computer-aided molecular design, 2020-02, Vol.34 (2), p.179-189
2020
Details
- Autor(en) / Beteiligte
- Titel
- Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4
- Ist Teil von
- Journal of computer-aided molecular design, 2020-02, Vol.34 (2), p.179-189
- Ort / Verlag
- Cham: Springer International Publishing
- Erscheinungsjahr
- 2020
- Link zum Volltext
- Quelle
- Alma/SFX Local Collection
- Beschreibungen/Notizen
- We describe a new template-based method for docking flexible ligands such as macrocycles to proteins. It combines Monte-Carlo energy minimization on the manifold, a fast manifold search method, with BRIKARD for complex flexible ligand searching, and with the MELD accelerator of Replica-Exchange Molecular Dynamics simulations for atomistic degrees of freedom. Here we test the method in the Drug Design Data Resource blind Grand Challenge competition. This method was among the best performers in the competition, giving sub-angstrom prediction quality for the majority of the targets.
- Sprache
- Englisch
- Identifikatoren
- ISSN: 0920-654XeISSN: 1573-4951DOI: 10.1007/s10822-019-00257-1Titel-ID: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_7553231
- Format
- –
- Schlagworte
- Animal Anatomy, Chemistry, Chemistry and Materials Science, Competition, Computer Applications in Chemistry, Computer simulation, Coordination compounds, Energy conservation, Histology, Ligands, Manifolds, Molecular docking, Molecular dynamics, Monte Carlo method, Morphology, Physical Chemistry, Proteins, Test procedures