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