//============================== // Please cite the following if you use MC-Sym: // 1) Major F et al. (1991) Science 253, 1255. // 2) Major F. (2003) Comp Sci Eng. 5, 44. //============================== // this MC-Sym script builds the H/ACA box small // nucleolar RNA pseudouridylation pocket from article: // Wu H, Feigon J. 2007 PNAS 104:6655-6660. // // Sequence numbering and chain IDs follow that of // PDB file 2P89. //========== Sequence ========== sequence( r A1 GGCCUUAGGAAACAGUUCGCUGUGCCGAAAGGUC ) sequence( r B35 UUCGGCUCUUCCUA ) //========== Cycles ========== ncm_15 = library( pdb( "MCSYM-DB/2_2/GCGC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A24:A25, B39:B40 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_16 = library( pdb( "MCSYM-DB/2_2/CCGG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A25:A26, B38:B39 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_17 = library( pdb( "MCSYM-DB/2_2/CGCG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A26:A27, B37:B38 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_18 = library( pdb( "MCSYM-DB/2_2/GAUC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A27:A28, B36:B37 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_19 = library( pdb( "MCSYM-DB/2_2/AAUU/*_s.pdb.gz" ) #1:#2, #3:#4 <- A28:A29, B35:B36 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) //=========== Backtrack =========== // assemble the whole structure: structure = backtrack( // start with P1S stem ncm_15 // complete P1S stem merge( ncm_16 2.0 ) merge( ncm_17 2.0 ) merge( ncm_18 2.0 ) merge( ncm_19 2.0 ) ) // ========= Constraints / Restraints ========= clash ( structure 2.0 !( pse || lp || hydrogen ) ) ribose_rst ( structure method = estimate, threshold = 2.0, pucker = C3p_endo, glycosyl = anti ) backtrack_rst ( structure method = exhaustive, width_limit = 25%, height_limit = 100% ) implicit_phosphate_rst( structure sampling = 90% ) // ========= Exploration Initialization ========= explore( structure option( time_limit = 12h, seed = 3210 ) //reference( pdb("2P89_01.pdb") ) rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) pdb( "HACA_P1S" zipped ) )