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SHAPE directed RNA folding.
Lorenz R, Luntzer D, Hofacker IL, Stadler PF, Wolfinger MT. Lorenz R, et al. Bioinformatics. 2016 Jan 1;32(1):145-7. doi: 10.1093/bioinformatics/btv523. Epub 2015 Sep 9. Bioinformatics. 2016. PMID: 26353838 Free PMC article.
Small-World Networks and RNA Secondary Structures.
Surujon D, Ponty Y, Clote P. Surujon D, et al. J Comput Biol. 2019 Jan;26(1):16-26. doi: 10.1089/cmb.2018.0125. Epub 2018 Oct 31. J Comput Biol. 2019. PMID: 30383444
RNA folding with hard and soft constraints.
Lorenz R, Hofacker IL, Stadler PF. Lorenz R, et al. Algorithms Mol Biol. 2016 Apr 23;11:8. doi: 10.1186/s13015-016-0070-z. eCollection 2016. Algorithms Mol Biol. 2016. PMID: 27110276 Free PMC article.