Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex

By Ilya A. Vakser. 1997

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Citations in the corpus

Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives (2012, background): “There are several other common applications of homology models: (1) studying the effect of mutations[111]; (2) identifying active and binding sites on protein (useful for ligand design) [112]; (3) searching for ligands of a given binding site (database mining)[113]; (4) designing novel ligands of a ”
A novel shape complementarity scoring function for protein‐protein docking (2003, methodology): “Some algorithms even use shape complementarity as the only component in their scoring functions.(21,22,29) The method by Ten Eyck and colleagues uses GSC and continuum electrostatics, which is more elaborate than the Coulombic electrostatics in ZDOCK.”
Protein-protein docking: from interaction to interactome. (2014, unknown): “The protein-protein docking category was introduced at CASP2 (43,65) and has been successfully continued in CAPRI.”
ZDOCK: An initial‐stage protein‐docking algorithm (2003, methodology): “5 GRAMM focuses on low-resolution docking, evaluating GSC with FFT. 6 PPD matches critical points by using geometric hashing.”
The HDOCK server for integrated protein–protein docking (2020, background): “…evolving from early ab initio template-free docking (which uses the structures of two molecules only to predict the structure of the complex) 7 – 9 to information-guided docking (which uses experimental binding information to constrain the sampling of putative binding modes during the docking…”
Protein docking using spherical polar Fourier correlations (2000, methodology): “63 To dock macromolecular complexes of this size, we expect similar measures would also be required with the spherical polar approach.”
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.”
Comparative protein structure modeling of genes and genomes. (2000, background): “In addition to the already listed applications, high quality models can be used for docking of small ligands (137) or whole proteins onto a given protein (186, 189).”