Evaluation of docking performance: comparative data on docking algorithms.

By M. Kontoyianni, Laura M McClellan, Glenn S. Sokol. Journal of Medicinal Chemistry, 2004

571 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Organic Chemistry

View Paper: https://www.semanticscholar.org/paper/6baaca1f4fed167d485526b3083221c648424fca

How researchers see this paper

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

In Computational Theory and Mathematics

In Molecular Biology

In Organic Chemistry

Citations in the corpus

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go (2008, methodology): “In the past decade, many comparative studies have been reported that evaluate the relative performance of the most popular programmes (Westhead et al., 1997; Bissantz et al., 2000; Perez and Ortiz, 2001; Stahl and Rarey, 2001; Terp et al., 2001; Doman et al., 2002; Diller and Li, 2003; Jenkins et al”
Using AutoDock for Ligand‐Receptor Docking (2008, background): “More recently, molecular docking has been combined with pharmacophore-based methods, while ligand-based screening has been shown to be increasingly useful in virtual screening when the structure of the target receptor is unknown (Kontoyianni et al. 2008).”
Computational Methods in Drug Discovery (2014, methodology): “GOLD has demonstrated better accuracy than most docking algorithms, except GLIDE, in various benchmark studies (Kellenberger et al., 2004; Kontoyianni et al., 2004; Li et al.,2010b). a.”
Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. (2006, background): “( 5 ) Metal-Ligand Interactions.”
High quality binding modes in docking ligands to proteins (2008, background): “19,20,46–48 The choice of a particular comparison procedure frequently depends on the particular problem, the data set and the programs under investigation.”
Sub‐angstrom modeling of complexes between flexible peptides and globular proteins (2010, background): “According to Kontoyianni et al .,63 the latter criterion is considered to be stringent (see Figure 2 for illustration of different peptide RMSDs).”
Software for molecular docking: a review (2017, methodology): “Contrary to GOLD, both LigandFit and Glide performed well with COX-2, a target with a mainly hydrophobic binding pocket (Kontoyianni et al. 2004).”
Comparing protein–ligand docking programs is difficult (2005, background): “Typically, docking programs work better on some targets than others 12,16,26,31 so a balanced assessment requires the test set to be large enough to cover diverse families, unless the point of the study is speciﬁcally to compare docking performance on a particular protein class (see for example, Hu…”