Coarse-grain Models of HIV-1 Nucleoids

These are PDB-format files that may be read by most molecular<br> graphics programs. The script JSmol.script will create a customized<br> view with appropriate radii, using JSmol. The PDB format is modified<br> in the following ways:<br> --coordinates are in nanometers<br> --RNA strands have atom name "P" and residue name "RNA"<br> --integrase subunits have atom name "CA" and residue name "IN"<br> --nucleocapsid subunits have atom name "N", and residue names<br> "NCO" for experimentally-observed positions and<br> "NCR" for randomly-placed positions Each file contains 25 instances of the nucleoid model.<br> Each model includes 2 gRNA strands, 2000 nucleocapsid subunits, and 140/0 integrase subunits.<br> Nine models are included in this release, exploring two types of variables:<br> 1) Three types of starting models: <br> "selfavoidingGag" assumes that the RNA forms a non-overlapping random walk on<br> the lattice of gag proteins in the immature virion<br> "overlappingGag" assumes a similar random walk, but the RNA strands may overlap<br> "random" assumes that RNA is released from gag and randomly fills the interior of<br> the virion before condensation <br> 2) Three assumptions about integrase interaction:<br> 35 integrase tetramers, 70 integrase dimers, and no integrase More information is available at:<br> http://ccsb.scripps.edu/latticenucleoid/HIVnucleoid