1 #ifndef VIENNA_RNA_PACKAGE_OLD_EPARS__ 2 #define VIENNA_RNA_PACKAGE_OLD_EPARS__ 3 /** 4 @file 1.8.4_epars.h 5 @ingroup energy_parameters_convert 6 @brief Free energy parameters for parameter file conversion 7 8 This file contains the free energy parameters used in ViennaRNAPackage 1.8.4. 9 They are summarized in: 10 11 D.H.Mathews, J. Sabina, M. ZUker, D.H. Turner 12 "Expanded sequence dependence of thermodynamic parameters improves 13 prediction of RNA secondary structure" 14 JMB, 288, pp 911-940, 1999 15 16 Enthalpies taken from: 17 18 A. Walter, D Turner, J Kim, M Lyttle, P M"uller, D Mathews, M Zuker 19 "Coaxial stckaing of helices enhances binding of oligoribonucleotides.." 20 PNAS, 91, pp 9218-9222, 1994 21 22 D.H. Turner, N. Sugimoto, and S.M. Freier. 23 "RNA Structure Prediction", 24 Ann. Rev. Biophys. Biophys. Chem. 17, 167-192, 1988. 25 26 John A.Jaeger, Douglas H.Turner, and Michael Zuker. 27 "Improved predictions of secondary structures for RNA", 28 PNAS, 86, 7706-7710, October 1989. 29 30 L. He, R. Kierzek, J. SantaLucia, A.E. Walter, D.H. Turner 31 "Nearest-Neughbor Parameters for GU Mismatches...." 32 Biochemistry 1991, 30 11124-11132 33 34 A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner 35 "Thermodynamic Study of Internal Loops in Oligoribonucleotides..." 36 Biochemistry 1991, 30, 6428--6435 37 */ 38 39 #define K0 273.15 40 #ifdef INF 41 #undef INF 42 #endif 43 #define INF 1000000 44 #define NBPAIRS 7 45 #define NST 0 /* Energy for nonstandard stacked pairs */ 46 #define DEF -50 /* Default terminal mismatch, used for I */ 47 /* and any non_pairing bases */ 48 #define NSM 0 /* terminal mismatch for non standard pairs */ 49 50 PRIVATE double Tmeasure_184 = 37 + K0; /* temperature of param measurements */ 51 PRIVATE double lxc37_184 = 107.856; /* parameter for logarithmic loop 52 energy extrapolation */ 53 54 PRIVATE int stack37_184[NBPAIRS+1][NBPAIRS+1] = 55 /* CG GC GU UG AU UA */ 56 { { INF, INF, INF, INF, INF, INF, INF, INF}, 57 { INF, -240, -330, -210, -140, -210, -210, NST}, 58 { INF, -330, -340, -250, -150, -220, -240, NST}, 59 { INF, -210, -250, 130, -50, -140, -130, NST}, 60 { INF, -140, -150, -50, 30, -60, -100, NST}, 61 { INF, -210, -220, -140, -60, -110, -90, NST}, 62 { INF, -210, -240, -130, -100, -90, -130, NST}, 63 { INF, NST, NST, NST, NST, NST, NST, NST}}; 64 65 /* enthalpies (0.01*kcal/mol at 37 C) for stacked pairs */ 66 /* different from mfold-2.3, which uses values from mfold-2.2 */ 67 PRIVATE int enthalpies_184[NBPAIRS+1][NBPAIRS+1] = 68 /* CG GC GU UG AU UA */ 69 { { INF, INF, INF, INF, INF, INF, INF, INF}, 70 { INF, -1060, -1340, -1210, -560, -1050, -1040, NST}, 71 { INF, -1340, -1490, -1260, -830, -1140, -1240, NST}, 72 { INF, -1210, -1260, -1460, -1350, -880, -1280, NST}, 73 { INF, -560, -830, -1350, -930, -320, -700, NST}, 74 { INF, -1050, -1140, -880, -320, -940, -680, NST}, 75 { INF, -1040, -1240, -1280, -700, -680, -770, NST}, 76 { INF, NST, NST, NST, NST, NST, NST, NST}}; 77 78 79 /* old values are here just for comparison */ 80 PRIVATE int oldhairpin37_184[31] = { /* from ViennaRNA 1.3 */ 81 INF, INF, INF, 410, 490, 440, 470, 500, 510, 520, 531, 82 542, 551, 560, 568, 575, 582, 589, 595, 601, 606, 83 611, 616, 621, 626, 630, 634, 638, 642, 646, 650}; 84 85 PRIVATE int hairpin37_184[31] = { 86 INF, INF, INF, 570, 560, 560, 540, 590, 560, 640, 650, 87 660, 670, 678, 686, 694, 701, 707, 713, 719, 725, 88 730, 735, 740, 744, 749, 753, 757, 761, 765, 769}; 89 90 PRIVATE int oldbulge37_184[31] = { 91 INF, 390, 310, 350, 420, 480, 500, 516, 531, 543, 555, 92 565, 574, 583, 591, 598, 605, 612, 618, 624, 630, 93 635, 640, 645, 649, 654, 658, 662, 666, 670, 673}; 94 95 PRIVATE int bulge37_184[31] = { 96 INF, 380, 280, 320, 360, 400, 440, 459, 470, 480, 490, 97 500, 510, 519, 527, 534, 541, 548, 554, 560, 565, 98 571, 576, 580, 585, 589, 594, 598, 602, 605, 609}; 99 100 PRIVATE int oldinternal_loop37_184[31] = { 101 INF, INF, 410, 510, 490, 530, 570, 587, 601, 614, 625, 102 635, 645, 653, 661, 669, 676, 682, 688, 694, 700, 103 705, 710, 715, 720, 724, 728, 732, 736, 740, 744}; 104 105 PRIVATE int internal_loop37_184[31] = { 106 INF, INF, 410, 510, 170, 180, 200, 220, 230, 240, 250, 107 260, 270, 278, 286, 294, 301, 307, 313, 319, 325, 108 330, 335, 340, 345, 349, 353, 357, 361, 365, 369}; 109 110 /* terminal mismatches */ 111 /* mismatch free energies for interior loops at 37C */ 112 PRIVATE int mismatchI37_184[NBPAIRS+1][5][5] = 113 { /* @@ */ 114 {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}}, 115 { /* CG */ 116 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 117 { 0, 0, 0, -110, 0}, /* A@ AA AC AG AU */ 118 { 0, 0, 0, 0, 0}, /* C@ CA CC CG CU */ 119 { 0, -110, 0, 0, 0}, /* G@ GA GC GG GU */ 120 { 0, 0, 0, 0, -70}},/* U@ UA UC UG UU */ 121 { /* GC */ 122 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 123 { 0, 0, 0, -110, 0}, /* A@ AA AC AG AU */ 124 { 0, 0, 0, 0, 0}, /* C@ CA CC CG CU */ 125 { 0, -110, 0, 0, 0}, /* G@ GA GC GG GU */ 126 { 0, 0, 0, 0, -70}},/* U@ UA UC UG UU */ 127 { /* GU */ 128 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 129 { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */ 130 { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */ 131 { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */ 132 { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */ 133 { /* UG */ 134 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 135 { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */ 136 { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */ 137 { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */ 138 { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */ 139 { /* AU */ 140 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 141 { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */ 142 { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */ 143 { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */ 144 { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */ 145 { /* UA */ 146 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 147 { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */ 148 { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */ 149 { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */ 150 { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */ 151 { /* @@ */ 152 { 90, 90, 90, 90, 90},{ 90, 90, 90, 90,-20},{ 90, 90, 90, 90, 90}, 153 { 90,-20, 90, 90, 90},{ 90, 90, 90, 90, 20}} 154 }; 155 156 /* mismatch free energies for hairpins at 37C */ 157 PRIVATE int mismatchH37_184[NBPAIRS+1][5][5] = 158 { /* @@ */ 159 {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}}, 160 { /* CG */ 161 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 162 { -90, -150, -150, -140, -180}, /* A@ AA AC AG AU */ 163 { -90, -100, -90, -290, -80}, /* C@ CA CC CG CU */ 164 { -90, -220, -200, -160, -110}, /* G@ GA GC GG GU */ 165 { -90, -170, -140, -180, -200}},/* U@ UA UC UG UU */ 166 { /* GC */ 167 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 168 { -70, -110, -150, -130, -210}, /* A@ AA AC AG AU */ 169 { -70, -110, -70, -240, -50}, /* C@ CA CC CG CU */ 170 { -70, -240, -290, -140, -120}, /* G@ GA GC GG GU */ 171 { -70, -190, -100, -220, -150}},/* U@ UA UC UG UU */ 172 { /* GU */ 173 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 174 { 0, 20, -50, -30, -30}, /* A@ AA AC AG AU */ 175 { 0, -10, -20, -150, -20}, /* C@ CA CC CG CU */ 176 { 0, -90, -110, -30, 0}, /* G@ GA GC GG GU */ 177 { 0, -30, -30, -40, -110}},/* U@ UA UC UG UU */ 178 { /* UG */ 179 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 180 { 0, -50, -30, -60, -50}, /* A@ AA AC AG AU */ 181 { 0, -20, -10, -170, 0}, /* C@ CA CC CG CU */ 182 { 0, -80, -120, -30, -70}, /* G@ GA GC GG GU */ 183 { 0, -60, -10, -60, -80}},/* U@ UA UC UG UU */ 184 { /* AU */ 185 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 186 { 0, -30, -50, -30, -30}, /* A@ AA AC AG AU */ 187 { 0, -10, -20, -150, -20}, /* C@ CA CC CG CU */ 188 { 0, -110, -120, -20, 20}, /* G@ GA GC GG GU */ 189 { 0, -30, -30, -60, -110}},/* U@ UA UC UG UU */ 190 { /* UA */ 191 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 192 { 0, -50, -30, -60, -50}, /* A@ AA AC AG AU */ 193 { 0, -20, -10, -120, -0}, /* C@ CA CC CG CU */ 194 { 0, -140, -120, -70, -20}, /* G@ GA GC GG GU */ 195 { 0, -30, -10, -50, -80}},/* U@ UA UC UG UU */ 196 { /* @@ */ 197 { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0}, 198 { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0}} 199 }; 200 201 /* mismatch energies in multiloops */ 202 PRIVATE int mismatchM37_184[NBPAIRS+1][5][5]; 203 204 /* these are probably junk */ 205 /* mismatch enthalpies for temperature scaling */ 206 PRIVATE int mism_H_184[NBPAIRS+1][5][5] = 207 { /* no pair */ 208 {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}}, 209 { /* CG */ 210 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 211 { DEF,-1030, -950,-1030,-1030}, /* A@ AA AC AG AU */ 212 { DEF, -520, -450, -520, -670}, /* C@ CA CC CG CU */ 213 { DEF, -940, -940, -940, -940}, /* G@ GA GC GG GU */ 214 { DEF, -810, -740, -810, -860}},/* U@ UA UC UG UU */ 215 { /* GC */ 216 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 217 { DEF, -520, -880, -560, -880}, /* A@ AA AC AG AU */ 218 { DEF, -720, -310, -310, -390}, /* C@ CA CC CG CU */ 219 { DEF, -710, -740, -620, -740}, /* G@ GA GC GG GU */ 220 { DEF, -500, -500, -500, -570}},/* U@ UA UC UG UU */ 221 { /* GU */ 222 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 223 { DEF, -430, -600, -600, -600}, /* A@ AA AC AG AU */ 224 { DEF, -260, -240, -240, -240}, /* C@ CA CC CG CU */ 225 { DEF, -340, -690, -690, -690}, /* G@ GA GC GG GU */ 226 { DEF, -330, -330, -330, -330}},/* U@ UA UC UG UU */ 227 { /* UG */ 228 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 229 { DEF, -720, -790, -960, -810}, /* A@ AA AC AG AU */ 230 { DEF, -480, -480, -360, -480}, /* C@ CA CC CG CU */ 231 { DEF, -660, -810, -920, -810}, /* G@ GA GC GG GU */ 232 { DEF, -550, -440, -550, -360}},/* U@ UA UC UG UU */ 233 { /* AU */ 234 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 235 { DEF, -430, -600, -600, -600}, /* A@ AA AC AG AU */ 236 { DEF, -260, -240, -240, -240}, /* C@ CA CC CG CU */ 237 { DEF, -340, -690, -690, -690}, /* G@ GA GC GG GU */ 238 { DEF, -330, -330, -330, -330}},/* U@ UA UC UG UU */ 239 { /* UA */ 240 { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */ 241 { DEF, -400, -630, -890, -590}, /* A@ AA AC AG AU */ 242 { DEF, -430, -510, -200, -180}, /* C@ CA CC CG CU */ 243 { DEF, -380, -680, -890, -680}, /* G@ GA GC GG GU */ 244 { DEF, -280, -140, -280, -140}},/* U@ UA UC UG UU */ 245 { /* nonstandard pair */ 246 {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF}, 247 {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF}} 248 }; 249 250 /* 5' dangling ends (unpaird base stacks on first paired base) */ 251 PRIVATE int dangle5_37_184[NBPAIRS+1][5]= 252 {/* @ A C G U */ 253 { INF, INF, INF, INF, INF}, /* no pair */ 254 { INF, -50, -30, -20, -10}, /* CG (stacks on C) */ 255 { INF, -20, -30, -0, -0}, /* GC (stacks on G) */ 256 { INF, -30, -30, -40, -20}, /* GU */ 257 { INF, -30, -10, -20, -20}, /* UG */ 258 { INF, -30, -30, -40, -20}, /* AU */ 259 { INF, -30, -10, -20, -20}, /* UA */ 260 { 0, 0, 0, 0, 0} /* @ */ 261 }; 262 263 /* 3' dangling ends (unpaired base stacks on second paired base */ 264 PRIVATE int dangle3_37_184[NBPAIRS+1][5]= 265 {/* @ A C G U */ 266 { INF, INF, INF, INF, INF}, /* no pair */ 267 { INF, -110, -40, -130, -60}, /* CG (stacks on G) */ 268 { INF, -170, -80, -170, -120}, /* GC */ 269 { INF, -70, -10, -70, -10}, /* GU */ 270 { INF, -80, -50, -80, -60}, /* UG */ 271 { INF, -70, -10, -70, -10}, /* AU */ 272 { INF, -80, -50, -80, -60}, /* UA */ 273 { 0, 0, 0, 0, 0} /* @ */ 274 }; 275 276 /* enthalpies for temperature scaling */ 277 PRIVATE int dangle3_H_184[NBPAIRS+1][5] = 278 {/* @ A C G U */ 279 { INF, INF, INF, INF, INF}, /* no pair */ 280 { 0, -740, -280, -640, -360}, 281 { 0, -900, -410, -860, -750}, 282 { 0, -740, -240, -720, -490}, 283 { 0, -490, -90, -550, -230}, 284 { 0, -570, -70, -580, -220}, 285 { 0, -490, -90, -550, -230}, 286 { 0, 0, 0, 0, 0} 287 }; 288 289 PRIVATE int dangle5_H_184[NBPAIRS+1][5] = 290 {/* @ A C G U */ 291 { INF, INF, INF, INF, INF}, /* no pair */ 292 { 0, -240, 330, 80, -140}, 293 { 0, -160, 70, -460, -40}, 294 { 0, 160, 220, 70, 310}, 295 { 0, -150, 510, 10, 100}, 296 { 0, 160, 220, 70, 310}, 297 { 0, -50, 690, -60, -60}, 298 { 0, 0, 0, 0, 0} 299 }; 300 301 302 /* constants for linearly destabilizing contributions for multi-loops 303 F = ML_closing + ML_intern*k + ML_BASE*u */ 304 /* old versions erroneously used ML_intern*(k-1) */ 305 PRIVATE int ML_BASE37_184 = 0; 306 PRIVATE int ML_closing37_184 = 340; 307 PRIVATE int ML_intern37_184 = 40; 308 309 /* Ninio-correction for asymmetric internal loops with branches n1 and n2 */ 310 /* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */ 311 PRIVATE int MAX_NINIO_184 = 300; /* maximum correction */ 312 PRIVATE int F_ninio37_184[5] = { 0, 40, 50, 20, 10 }; /* only F[2] used */ 313 314 /* stabilizing contribution due to special hairpins of size 4 (tetraloops) */ 315 316 PRIVATE char Tetraloops_184[1400] = /* place for up to 200 tetra loops */ 317 "GGGGAC " 318 "GGUGAC " 319 "CGAAAG " 320 "GGAGAC " 321 "CGCAAG " 322 "GGAAAC " 323 "CGGAAG " 324 "CUUCGG " 325 "CGUGAG " 326 "CGAAGG " 327 "CUACGG " 328 "GGCAAC " 329 "CGCGAG " 330 "UGAGAG " 331 "CGAGAG " 332 "AGAAAU " 333 "CGUAAG " 334 "CUAACG " 335 "UGAAAG " 336 "GGAAGC " 337 "GGGAAC " 338 "UGAAAA " 339 "AGCAAU " 340 "AGUAAU " 341 "CGGGAG " 342 "AGUGAU " 343 "GGCGAC " 344 "GGGAGC " 345 "GUGAAC " 346 "UGGAAA " 347 ; 348 349 PRIVATE int TETRA_ENERGY37_184[200] = { 350 -300, -300, -300, -300, -300, -300, -300, -300, -300, -250, -250, -250, 351 -250, -250, -200, -200, -200, -200, -200, -150, -150, -150, -150, -150, 352 -150, -150, -150, -150, -150, -150}; 353 354 PRIVATE int TETRA_ENTH37_184 = -400; 355 356 PRIVATE char Triloops_184[241] = ""; 357 358 PRIVATE int Triloop_E37_184[40]; 359 360 /* penalty for AU (or GU) terminating helix) */ 361 /* mismatches already contain these */ 362 PRIVATE int TerminalAU_184 = 50; 363 364 /* penalty for forming a bi-molecular duplex */ 365 PRIVATE int DuplexInit_184 = 410; 366 367 #endif 368