//============================== // 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_10 = library( pdb( "MCSYM-DB/2_2/ACGU/*_s.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, A22:A23 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_11 = library( pdb( "MCSYM-DB/2_2/CAUG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A13:A14, A21:A22 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_12 = library( pdb( "MCSYM-DB/2_2/AGCU/*_s.pdb.gz" ) #1:#2, #3:#4 <- A14:A15, A20:A21 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_13 = library( pdb( "MCSYM-DB/2_2/GUGC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A15:A16, A19:A20 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_14 = library( pdb( "MCSYM-DB/4/UUCG/*_1.pdb.gz" ) #1:#4 <- A16:A19 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //=========== Backtrack =========== // assemble the whole structure: structure = backtrack( // start with P2 stem ncm_10 // complete P2 stem merge( ncm_11 2.0 ) merge( ncm_12 2.0 ) merge( ncm_13 2.0 ) merge( ncm_14 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_P2" zipped ) )