Protein–protein docking benchmark 2.0: An update
By J. Mintseris, K. Wiehe, Brian G. Pierce, Robert Anderson, Rong Chen, Joël Janin, Zhiping Weng. Proteins: Structure, Function, and Bioinformatics, 2005
301 citations recorded by the source corpus.
Subfields: Molecular Biology, Radiology, Nuclear Medicine and Imaging
View Paper: https://www.semanticscholar.org/paper/cb619e75b09d92c8ef2e7aedac16aa0925c15e74
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In Molecular Biology
- Shengyou Huang
- Alexandre M. J. J. Bonvin
- Jeffrey J. Gray
- Xiaoqin Zou
- Juan Fernández-Recio
- D. Ritchie
- M. V. van Dijk
- Tanja Kortemme
In Radiology, Nuclear Medicine and Imaging
- Alexandre M. J. J. Bonvin
- Haim J. Wolfson
- Ruth Nussinov
- Jeffrey J. Gray
- Efrat Mashiach
- Juan Fernández-Recio
- Nelly Andrusier
- Brian G. Pierce
Citations in the corpus
- Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants (2021, background): “Based on levels of binding conformational changes and previously defined criteria, 38 the cases had unbound docking difficulty classifications of Rigid (95 cases), Medium difficulty (34 cases) and Difficult (23 cases).”
- MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15–19 (2010, methodology): “…been extensively validated for binding mode prediction using three unbound docking test sets, including a combined test set from the three benchmarks (Benchmark 0.0, 1.0, and 2.0) prepared by Weng and Co-workers,36,37 the ZDOCK decoy set,23,38 and the Roset-taDock unbound perturbation decoy set.”
- A protein–DNA docking benchmark (2008, methodology): “We have constructed a benchmark of 47 protein–DNA test cases in a similar manner as has been done for protein–protein docking (5).”
- An iterative knowledge‐based scoring function for protein–protein recognition (2008, methodology): “66,67 If the same PDB entry appears in two or more benchmarks, only the one in the later benchmark was kept.”
- Recent progress and future directions in protein-protein docking. (2008, background): “Although both Tolb, and Pal change conformation on binding, the backbone motions are relatively small (0.97Å and 0.41Å RMS for the TolB -propeller and Pal domains, respectively), with much of the overall TolB conformational change appearing allosterically in the N-terminal domain [58].”
- Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2 (2011, background): “[30], is based on the magnitude of backbone conformational changes between the bound and unbound conformations.”
- FireDock: a web server for fast interaction refinement in molecular docking (2008, methodology): “The FireDock method was extensively tested (16) on docking candidates generated by the PatchDock method (10,21) for cases from benchmark 1.0 and 2.0 (28,29).”