ArticleJournal of chemical information and modeling2021
Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing.
Article in Journal of chemical information and modeling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 20 citations in OpenAlex.
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- Innovative Approaches in Molecular Docking for the Discovery of Novel Inhibitors Against Alzheimer's Disease.Current Alzheimer research · 2025Review
- The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.Nature protocols · 2024Review
- Modeling Protein-Glycan Interactions with HADDOCK.Journal of chemical information and modeling · 2024Article
- A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance.Life science alliance · 2023Article
- Response and Resistance to Trametinib in MAP2K1-Mutant Triple-Negative Melanoma.International journal of molecular sciences · 2023Article
- Bioprospecting microbes and enzymes for the production of pterocarpans and coumestans.Frontiers in bioengineering and biotechnology · 2023Review
- Investigation of the binding and dynamic features of A.30 variant revealed higher binding of RBD for hACE2 and escapes the neutralizing antibody: A molecular simulation approach.Computers in biology and medicine · 2022Article
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- The Omicron (B.1.1.529) variant of SARS-CoV-2 binds to the hACE2 receptor more strongly and escapes the antibody response: Insights from structural and simulation data.International journal of biological macromolecules · 2022Article
- Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor.Computers in biology and medicine · 2021Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small-molecule docking remains one of the most valuable computational techniques for the structure prediction of protein-small-molecule complexes. It allows us to study the interactions between compounds and the protein receptors they target at atomic detail in a timely and efficient manner. Here, we present a new protocol in HADDOCK (High Ambiguity Driven DOCKing), our integrative modeling platform, which incorporates homology information for both receptor and compounds. It makes use of HADDOCK's unique ability to integrate information in the simulation to drive it toward conformations, which agree with the provided data. The focal point is the use of shape restraints derived from homologous compounds bound to the target receptors. We have developed two protocols: in the first, the shape is composed of dummy atom beads based on the position of the heavy atoms of the homologous template compound, whereas in the second, the shape is additionally annotated with pharmacophore data for some or all beads. For both protocols, ambiguous distance restraints are subsequently defined between those beads and the heavy atoms of the ligand to be docked. We have benchmarked the performance of these protocols with a fully unbound version of the widely used DUD-E (Database of Useful Decoys-Enhanced) dataset. In this unbound docking scenario, our template/shape-based docking protocol reaches an overall success rate of 81% when a reliable template can be identified (which was the case for 99 out of 102 complexes in the DUD-E dataset), which is close to the best results reported for bound docking on the DUD-E dataset.
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