ZDOCK: An initial‐stage protein‐docking algorithm

By Rong Chen, Li Li, Zhiping Weng. 2003

1,408 citations recorded by the source corpus.

Subfields: Molecular Biology, Radiology, Nuclear Medicine and Imaging

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Citations in the corpus

DockQ: A Quality Measure for Protein-Protein Docking Models (2016, methodology): “Thus, the scoring part of CAPRI [8] and benchmarks of scoring functions for docking [11,10,12,13] only focuses on the ability to select good models according to the CAPRI classification, completely ignoring the potential useful information in the lower ranked models in assessing the ability to…”
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants (2021, methodology): “…up to 10 Å L-RMSD), medium and high-accuracy models are more reflective of previously utilized model accuracy cutoffs, such as the 2.5 Å I-RMSD cutoff used for near-native models by Chen and Weng 40 ; accordingly, multiple studies have used the medium accuracy cutoff to identify near-native models.”
The HADDOCK web server for data-driven biomolecular docking (2010, methodology): “We recommend that HADDOCK parameter files be deposited along with HADDOCK-generated structures in the Protein Data Bank.”
Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds (2016, background): “In later FFT based methods the scoring function has been expanded to include electrostatic and solvation terms [6, 7], and more recently structure-based interaction potentials [8, 9], substantially improving the accuracy of docked structures.”
An iterative knowledge‐based scoring function for protein–protein recognition (2008, methodology): “14,15 The decoys were generated from the Benchmark 0.0 of 49 protein–protein complexes by Weng and coworkers, using unbound docking via the ZDOCK software.”
RDOCK: Refinement of rigid‐body protein docking predictions (2003, background): “34 In addition to being more consistent, smaller (cid:5) (such as 6°) led to many more hits.”
Integrating statistical pair potentials into protein complex prediction (2007, background): “(4)], thus allowing the calculation to be completed in a single FFT correlation.”
Protein–protein docking benchmark version 4.0 (2010, background): “49 2599 1OC0_A:B E 1B3K_A Plasminogen activator inhibitor-1 2JQ8_A(4) Vitronectin Somatomedin B domain 1 1312 1OYV_A:I E 1SCD_A Subtilisin Carlsberg 1PJU_A Two-headed tomato inhibitor-II 0.”