EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases

By Y. Pang, E. Perola, Kun Xu, F. Prendergast. 2001

108 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Computational Chemistry & Drug Discovery

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 Computational Chemistry & Drug Discovery

Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, methodology): “…Search eHiTS [28] AutoDock [34] FRED [30] Gold [35] Surflex-Dock [31] PRO_LEADS [44] DOCK [32] EADock [45] GLIDE [37] ICM [46] EUDOC [38] LigandFit [47] FlexX [39] Molegro Virtual Docker [48] Hammerhead [40] CDocker [49] Flog [41] GlamDock [50] SLIDE [42] PLANTS [51] ADAM [43]…”
Comparative evaluation of eight docking tools for docking and virtual screening accuracy (2004, background): “Detailed benchmarks ( 100 Protein Data Bank (PDB)– ligand complexes) are only reported for a few docking tools.(12,14,16,18,24,38) The purpose of the current study is to provide independent benchmarks for widely used docking programs.”
Advances and Challenges in Protein-Ligand Docking (2010, methodology): “Examples of docking programs that use shape matching include DOCK [1], FRED [44], FLOG [45], EUDOC [46], LigandFit [47], Surflex [48], MS-DOCK [49], and MDock [32,33].”
Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, background): “Historically, most of these comparisons have been made in terms of their ability to reproduce the X-ray pose of selected ligands [8, 18, 21, 32-50], their capability to predict binding free energies from the best-scored pose [16, 21, 24, 27, 28, 35, 51-56], or their ability to identify known binders”
A new test set for validating predictions of protein–ligand interaction (2002, methodology): “Reasons to exclude protein structures can be: (1) the presence of factual and structural errors in the original PDB file; (2) an inconsistency between the electron density in the binding site and the reported position and conformation of the ligand; or, an unlikely conformation of the ligand; (3) th”
GEMDOCK: A generic evolutionary method for molecular docking (2004, background): “The treatment of structure water molecules in docking and drug-screening studies is still under investigation.(20,23,44) Figures 5(A) and 7(A) show the docked conformations of 2 -adenylic acid (2AM) into a ribonuclease (6rnt) following removal and retention of the structure water molecules, Fig.”
Efficient docking of peptides to proteins without prior knowledge of the binding site (2002, background): “A large number of programs have been developed to this end, for example, DOCK (Shoichet and Kuntz 1993), AutoDock (Morris et al. 1996, 1998), and some more recent algorithms described in Budin et al. (2001) and Pang et al. (2001) .”
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, methodology): “Examples are oﬀered by FLOG (Miller et al., 1994), EUDOC (Pang et al., 2001), MS-DOCK (Sauton et al., 2008).”