A protein–protein docking benchmark

By Rong Chen, J. Mintseris, Joël Janin, Zhiping Weng. Proteins: Structure, Function, and Bioinformatics, 2003

362 citations recorded by the source corpus.

Subfields: Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/ba5498c48fd2fd8af7ba5c1930ef8596022e4798

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Shengyou Huang
2. Alexandre M. J. J. Bonvin
3. Xiaoqin Zou
4. Jeffrey J. Gray
5. Brian G. Pierce
6. David Baker
7. Zhiping Weng
8. Haim J. Wolfson

In Radiology, Nuclear Medicine and Imaging

1. Shengyou Huang
2. Xiaoqin Zou
3. Alexandre M. J. J. Bonvin
4. Sandor Vajda
5. Brian G. Pierce
6. Dima Kozakov
7. Haim J. Wolfson
8. Ruth Nussinov

Citations in the corpus

• 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.”
• Dockground: A comprehensive data resource for modeling of protein complexes (2018, background): “Because of that, the datasets of unbound structures corresponding to the co-crystallized complexes 16,18–20 are essential for the development and validation of docking approaches.”
• Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. (2003, background): “35 For each target, the all-atom score of 1000 decoys is plotted as a function of the rmsd from the native structure (calculated over the C a atoms of the smaller docking partner in the fixed coordinate frame of the larger partner).”
• Assessing predictions of protein–protein interaction: The CAPRI experiment (2005, background): “Cases where the PDB contains entries for both a complex and its free components are relatively few, and a selection of these is available to benchmark docking methods (Chen et al. 2003).”
• FireDock: Fast interaction refinement in molecular docking (2007, methodology): “10,11 The refinement stage performed by FireDock clearly improves the ranking of PatchDock for these cases.”
• What Method to Use for Protein-Protein Docking? (2019, background): “The protein-protein benchmark set, collected by the Weng lab [8–11], has become well established for testing docking methods.”
• CAPRI: A Critical Assessment of PRedicted Interactions (2003, neutral): “19”
• PIPER: An FFT‐based protein docking program with pairwise potentials (2006, positive): “32,33 For comparison we also docked the antibody–antigen pairs in the benchmark set 1.”
• ZDOCK: An initial‐stage protein‐docking algorithm (2003, methodology): “We used version 0.0 of a benchmark developed in our laboratory, 22 which contained 23 enzyme-inhibitor, 16 antibody-antigen, and 10 other types of test cases.”
• PatchDock and SymmDock: servers for rigid and symmetric docking (2005, background): “Our experience in the CAPRI (22) and other benchmarks (21) indicates that a near-native result is found among the top 100, and very often among the top 10 solutions.”
• New additions to the ClusPro server motivated by CAPRI (2017, background): “32–35 Docking of the protein pairs in the protein–protein benchmark 32–35 has shown that none of the above generic sets of weights works well for every protein, and the number of near-native structures generated substantially depends on selecting the right parameters.”
• How Good is Automated Protein Docking? (2013, background): “26 The “Other Mode” targets the so-called “other” type of complexes that primarily occur in signal transduction pathways,27 and generally have substantially less perfect shape and electrostatic complementarity than the enzyme–inhibitor complexes.”