Ontology highlight
ABSTRACT:
SUBMITTER: Dolenc J
PROVIDER: S-EPMC548343 | biostudies-literature | 2005
REPOSITORIES: biostudies-literature
Dolenc Jozica J Oostenbrink Chris C Koller Joze J van Gunsteren Wilfred F WF
Nucleic acids research 20050201 2
Molecular dynamics simulations have been performed on netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of the ligands free in solution and when bound to DNA, the mobility and the hydrogen-bonding patterns of t ...[more]