Table 1.
A Tabular overview with some basic information about the various RNA design programs
| Programs | Webserver | Source code | Extension to pseudoknots | Multitarget capability | Remarks |
|---|---|---|---|---|---|
| General | |||||
| AntaRNA [44, 45] | ✓ | ✓ | ✓ | ||
| RNAiFold [42, 43] | ✓ | ✓ | ✓ | Experience in biology ‘wet laboratory’ | |
| RNAinverse [1] | ✓ | ✓ | First program developed; experience in biology ‘wet laboratory’ | ||
| NUPACK [35, 36] | ✓ | ✓ | Optional multistranded target structures; experience in biology ‘wet laboratory’ | ||
| INFO-RNA [33] | ✓ | ✓ | |||
| RNA-SSD [34] | ✓ | ||||
| Frnakenstein [39] | ✓ | ✓ | |||
| ERD [40, 41] | ✓ | ✓ | ✓ | ||
| MODENA [38] | ✓ | ✓ | ✓ | ||
| Shape aware | |||||
| IncaRNAfbinv [52] | ✓ | ✓ | Fragment selection enabled; experience in RNA detection | ||
| RNAfbinv [51] | ✓ | Fragment selection enabled | |||
| RNAexinv [48] | ✓ | No user-selected fragment | |||
| Adaptive sampling | |||||
| IncaRNAfbinv [52] | ✓ | ✓ | Global–local approach; experience in RNA detection | ||
| IncaRNAtion [47] | ✓ | Global–local approach | |||
| RNA-ensign [46] | ✓ | Global approach | |||
| Specialized | |||||
| Nanofolder [12] | ✓ | ✓ | Nanostructures; multistranded RNA; experience in biology ‘wet laboratory’ | ||
| CDSfold [54] | ✓ | ✓ | Design of protein-coding sequence | ||
| RNAdesign [56] | ✓ | ✓ | |||
| EternaBot [57] | ✓ | Design rules set by Eterna players | |||
| RNA-redesign [58] | ✓ | Three-dimensional: fixed backbone |