Clustering biomolecular complexes by residue contacts similarity
By João P. G. L. M. Rodrigues, Mikael E. Trellet, Christophe Schmitz, Panagiotis L. Kastritis, Ezgi Karaca, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin. 2012
123 citations recorded by the source corpus.
Subfields: Molecular Biology
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In Molecular Biology
- Alexandre M. J. J. Bonvin
- Zeynep Kurkcuoglu
- M. V. van Dijk
- João P. G. L. M. Rodrigues
- Rodrigo Vargas Honorato
- Anna Vangone
- Jorge Roel‐Touris
- Brian G. Pierce
Citations in the corpus
- The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. (2016, methodology): “In addition, the Expert interface gives control over the Sampling Parameters, including namely the number of structures to generate at each stage and whether or not to perform solvated docking [20,21,23].”
- Contacts-based prediction of binding affinity in protein–protein complexes (2015, background): “Next to their use in scoring, contacts have been introduced as a way to cluster docking solutions based on the fraction of common inter-residue contacts among a set of decoys ( Rodrigues et al., 2012 ).”
- Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants (2021, methodology): “…such as explicit side chain flexibility during docking searches, 8 use of normal mode analysis to represent protein flexibility, 9,10 clustering 11,12 or re-scoring 13 – 16 docking models to improve ranking of near-native models, and use of experimental data as restraints for docking 17 have led…”
- Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems (2019, methodology): “FCC clustering was used with 0.75 cut-off and a minimum cluster size of 4.”
- MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing (2019, methodology): “The final resulting models are clustered based on the fraction of common contacts (FCC) (Rodrigues et al., 2012) using a 0.6 cutoff (i.e., two models belonging to the same cluster share at least 60% of contacts) and a minimum of four models per cluster, which is the default clustering protocol in…”