1at8

Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.

THEORETICAL MODEL OF THE REV BINDING ELEMENT (RBE, 30 RIBONUCLEOTIDE FRAGMENT) OF HUMAN IMMUNODEFICIENCY VIRUS-1 COMPLEXED WITH NEOMYCIN B

spinqualitylabelsall models 1at8 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights For a guided tour on the structure components use FirstGlance. Resources: FirstGlance, PDBsum, ProSAT Publication Abstract from PubMed An approach to the modeling of ligand-RNA complexes has been developed by combining three-dimensional structure-activity relationship (3D-SAR) computations with a docking protocol. The ability of 3D-SAR to predict bound conformations of flexible ligands was first assessed by attempting to reconstruct the known, bound conformations of phenyloxazolines complexed with human rhinovirus 14 (HRV14) RNA. Subsequently, the same 3D-SAR analysis was applied to the identification of bound conformations of aminoglycosides which associate with the Rev-binding element (RBE) RNA. Bound conformations were identified by parsing ligand conformational data sets with pharmacophores determined by the 3D-SAR analysis. These "bioactive" structures were docked to the receptor RNA, and optimization of the complex was undertaken by extensive searching of ligand conformational space coupled with molecular dynamics computations. The similarity between the bound conformations of the ligand from the 3D-SAR analysis and those found in the docking protocol suggests that this methodology is valid for the prediction of bound ligand conformations and the modeling of the structure of the ligand-RNA complexes. Modeling RNA-ligand interactions: the Rev-binding element RNA-aminoglycoside complex.,Leclerc F, Cedergren R J Med Chem. 1998 Jan 15;41(2):175-82. PMID:9457241 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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