Patent ID: 6947845

Claim:
A method of identifying a molecule that binds to a large ribosomal subunit, the method comprising the steps of: (a) providing a molecular model comprising one or more target regions selected from the group consisting of at least a portion of (i) an anisomycin binding site, (ii) an azithromycin binding site, (iii) a blasticidin binding site, (iv) a carbomycin A binding site, (v) an erythromycin binding site, (vi) a linezolid binding site, (vii) a sparsomycin binding site, (viii) a spiramycin binding site, (ix) a tylosin binding site, and (x) a virginiamycin M binding site, wherein the molecular model is made; (1) from the atomic co-ordinates for the Haloarcula marismortui large ribosomal subunit found on Disk 1 under file names ANISOMYCIN.PDB, azithromycin.pdb, BLASTICIDIN.PDB, CARBOMYCIN.PDB, erythromycin.pdb, linezolid.pdb, SPARSOMYCIN.PDB, SPIRAMYCIN.PDB, TYLOSIN.PDB, or VIRGINAMYCIN.PDB, or found on Disk 1, under FOLDERB, under file names ANISOMYC.PDB, BLASTICI.PDB, CARBOMYC.PDB, SPARSOMY.PDB, SPIRAMYC.PDB, TYLOSIN.PDB, VIRGINIA.PDB, or found on Disk 1, under FOLDERC, under file names AZITHROM.PDB, or LINEZOLI.PDB, or (2) from atomic co-ordinates derived by molecular modeling using the atomic coordinates for the Haloarcula marismortui large ribosomal subunit found on Disk 1 under file names ANISOMYCIN.PDB. azithromycin.pdb, BLASTICIDIN. PDB, CARBOMYCIN.PDB. erythromycin.pdb, linezolid.pdb, SPARSOMYCIN.PDB, SPIRAMYCIN.PDB, TYLOSIN.PDB, or VIRGINAMYCIN.PDB, or found on Disk 1, under FOLDERB, under file names ANISOMYC.PDB, BLASTICI.PDB, CARBOMYC.PDB, SPARSOMY.PDB, SPIRAMYC.PDB, TYLOSIN.PDB, VIRGINIA.PDB, or found on Disk 1, under FOLDERC, under file names AZITHROM.PDB, or LINEZOLI.PDB; (b) using the molecular model to identify a candidate molecule that can bind to the molecular model; and (c) producing the candidate molecule identified in step (b).