Developing a dynamic pharmacophore model for HIV-1 integrase.

By Heather A. Carlson, K. Masukawa, K. Rubins, Fredric D. Bushman, William L. Jorgensen, Roberto D. Lins, James M. Briggs, James Andrew McCammon. 2000

232 citations recorded by the source corpus.

Subfields: Infectious Diseases, Molecular Biology, Virology, 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 Infectious Diseases

In Molecular Biology

In Virology

In Computational Chemistry & Drug Discovery

Citations in the corpus

A Role for Fragment-Based Drug Design in Developing Novel Lead Compounds for Central Nervous System Targets (2015, methodology): “The flexible binding pocket is prepared using a pharmacophore, after molecular dynamics simulations identify possible conformational changes within the receptor (28).”
Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations (2015, unknown): “88 Comparison to other receptor-based pharmacophore methods In the absence of small-molecule inhibitors (or natural substrates), others have also used features of the receptor to build pharmacophores (91, 92, 135, 136, 190-193); like these, the “exemplars” we describe here are essentially receptor-b”
In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling (2007, background): “…of targets such as protein kinase C (Wang et al ., 1994), farnesyltrans-ferase (Kaminski et al ., 1997), HIV integrase (Nicklaus et al ., 1997; Carlson et al ., 2000), endothelial differentiation gene receptor antagonists (Koide et al ., 2002), urotensin antagonists (Flohr et al ., 2002),…”
Advances and Challenges in Protein-Ligand Docking (2010, methodology): “simulations, Monte Carlo simulations, or structure prediction have also been used to account for protein flexibility [35–43].”
Combining docking and molecular dynamic simulations in drug design (2006, methodology): “Carlson et al. 102 developed ‘‘dynamic’’ pharmacophore models of HIV-1 integrase using several snapshots from an MD simulation.”
Computer-aided drug-discovery techniques that account for receptor flexibility. (2010, unknown): “A composite pharmacophore model based on these many characterizations is then generated, and ligand databases are searched for compounds with complementary chemical features [12,15,34].”
Protein flexibility in ligand docking and virtual screening to protein kinases. (2004, methodology): “Multiple structures generated through MD simulations were used to build a receptorbased pharmacophore model for the HIV-1 integrase.(29) In the search for the correct ligand– receptor conformation, the relaxed complex method(30,31) uses an ensemble of structures generated through MD simulations of t”
Molecular docking: a powerful approach for structure-based drug discovery. (2011, background): “Still another way to deal with the protein flexibility is to use an ensemble of protein conformations, which corresponds to the theory of conformer selection [113, 114].”
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking (2006, background): “26,27 On the basis of the conformational ensemble from MD simulations.”