Protein docking using spherical polar Fourier correlations

By D. Ritchie, G. Kemp. Proteins: Structure, Function, and Bioinformatics, 2000

604 citations recorded by the source corpus.

Subfields: Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/c22fa752108a5271e3b17b2c3fe78ad0eeab1e08

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Citations in the corpus

pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking (2007, methodology): “HEX 14 is an alternative method that uses polar Fourier correlations to accelerate docking calculations.”
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment (2019, neutral): “Interestingly, a number of groups relied on reputable CAPRI docking servers such as CLUSPRO 57 and/or algorithms such ZDOCK, 35 or HEX, 70 developed by other groups, to generate their docking poses.”
Chemical shift-based methods in NMR structure determination (2018, methodology): “CamDock performs ab initio modeling of protein complexes using the Chord program [152] which is based on the HEX [153] approach in its use of a spherical harmonics-based representation of protein surfaces.”
Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry (2016, methodology): “Following the original Hex docking algorithm, A ð r Þ and B ð r Þ consist of linear combinations of three-dimensional interior and surface skin density functions (Ritchie & Kemp, 2000).”
The HADDOCK web server for data-driven biomolecular docking (2010, methodology): “A number of other docking servers have already been developed, such as ClusPro 17 , GRAMM-X 18 , PatchDock/FireDock 19–21 , Hex 22,23 and RosettaDock 24 .”
Protein–protein docking with a reduced protein model accounting for side‐chain flexibility (2003, methodology): “2000), or Fourier correlation techniques (Katchalski-Katzir et al. 1992; Meyer et al. 1996; Gabb et al. 1997; Vakser 1997; Ritchie and Kemp 2000; Chen and Weng 2002) to identify an optimal overlap between complementary surface layers of the protein partners.”
The scoring of poses in protein-protein docking: current capabilities and future directions (2013, methodology): “These range from composite scoring functions using a linear combination of terms, usually models of the underlying physical phenomena at play [52-65], to methods derived from the statistics of structural databases [63,66-70], docking decoys [71-75], experimental binding energies [76], methods based ”
FireDock: a web server for fast interaction refinement in molecular docking (2008, methodology): “The candidate solutions for FireDock can be generated by rigid-body docking methods, such as PatchDock (10,21), methods that use Fast Fourier Transform (FFT) such as ZDOCK (20,36), GRAMM-X (26), Hex (27), etc.”
RDOCK: Refinement of rigid‐body protein docking predictions (2003, methodology): “Most previous methods assumed known binding site information, and/or used 10 unbound test cases.(5,7,9,11,14-18,22,38) Others focused on discriminating against low RMSD false positives.”