//============================== // 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_01 = library( pdb( "MCSYM-DB/2_2/GGUC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A33:A34 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_2/GCGU/*_s.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A32:A33 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/CCGG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A31:A32 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/CUAG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A30:A31 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) //=========== Backtrack =========== // assemble the whole structure: structure = backtrack( // start with P1 stem ncm_01 // complete P1 stem merge( ncm_02 2.0 ) merge( ncm_03 2.0 ) merge( ncm_04 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_P1" zipped ) )