A novel shape complementarity scoring function for protein‐protein docking

By Rong Chen, Zhiping Weng. Proteins: Structure, Function, and Bioinformatics, 2003

297 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/28d773f1653a00be35b3fe9081d226f55dec8b42

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Citations in the corpus

RDOCK: Refinement of rigid‐body protein docking predictions (2003, background): “33 At a 6° rotational sampling density, PSC retains at least one hit in the top 2,000 predictions for 42 out of 49 test cases in the benchmark.”
An iterative knowledge‐based scoring function for protein–protein recognition (2008, methodology): “14 The default parameters except the number of output predictions (set to 1000, here) in ZDOCK 2.1 were used in the present work.”
Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2 (2015, methodology): “ZDOCK is an FFT-based rigid-body docking algorithm that performs a grid-based exhaustive search with a 15° or 6° rotational sampling in three-dimensional (3D) rotational space and a 1.2 Å sampling in the 3D translational space [32,33,38,52].”
ZDOCK: An initial‐stage protein‐docking algorithm (2003, methodology): “The resulting scoring function is tested on the same benchmark 22 and proves superior to PSC alone 23 and the GSC (cid:2) DE (cid:2) ELEC scoring function in our previous study.”
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.”
Global rigid body modeling of macromolecular complexes against small-angle scattering data. (2005, unknown): “The pairwise shape complementarity scoring function maximizing the total number of atom pairs between the receptor and the ligand within the distance cutoff is developed (53) and can be optimized together with disolvation free energy and electrostatics (54).”
ClusPro: a fully automated algorithm for protein-protein docking (2004, methodology): “The scoring function of ZDOCK is more intricate, hence ZDOCK typically has a better ratio of true positives to false positives than using the simpler scoring function of DOT.”