TY - JOUR
T1 - Small changes in free energy assignments for unpaid bases do not affect predicted secondary structures in single stranded RNA
AU - Nussinov, Ruth
AU - Tinoco, Ignacio
AU - Jacobson, Ann B.
N1 - Funding Information:
ACKNOWLEDGEMENTS We wish to thank K. Wiley and especially S. Wong from the laboratory of Chemical Blodynamics Computer Center for their help and advice in program modification. We are indebted to J. L. Dilsworth from the Lawrence Berkeley Laboratory Computer Center who made the2600 nucleotide runpossible. Without histime and help this project could not have been executed. This work was supported In part by National Institutes of Health Grant GH 10840 (IT), Al 15273(AJ) and by the Division of Biomedical and Environmental Research of the U.S. Department of Energy under Contract No. W-y'tOJ-Eng. ^8.
PY - 1982/1/11
Y1 - 1982/1/11
N2 - We present extensive calculations of the secondary structure of mRNA which point to its insensitivity to small changes in the free energy assignments of single stranded regions. Truncating the free energies of hairpin loops, bulges, internal loops and multibranched junctions to two significant digits yields structures nearly identical to those generated using three digit values. The results show that one can safely use truncated values in RNA folding calculations. The implementation of these results enabled us to carry out second ary structure calculations on 2600 nucleotides in a single computer run.
AB - We present extensive calculations of the secondary structure of mRNA which point to its insensitivity to small changes in the free energy assignments of single stranded regions. Truncating the free energies of hairpin loops, bulges, internal loops and multibranched junctions to two significant digits yields structures nearly identical to those generated using three digit values. The results show that one can safely use truncated values in RNA folding calculations. The implementation of these results enabled us to carry out second ary structure calculations on 2600 nucleotides in a single computer run.
UR - http://www.scopus.com/inward/record.url?scp=0020053976&partnerID=8YFLogxK
U2 - 10.1093/nar/10.1.341
DO - 10.1093/nar/10.1.341
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AN - SCOPUS:0020053976
SN - 0305-1048
VL - 10
SP - 341
EP - 349
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - 1
ER -