Table 1.
Computational tools for structure-based protein engineering
| Target property | Tool | Distributiona | Obligatory inputsb | Outputsc | Section | Runtimed | Application statuse | Link |
|---|---|---|---|---|---|---|---|---|
| Allostery | VisualCMAT [46] | WS | – | R, 3D, D | 2.1 | I / M | 0 / 6 | https://biokinet.belozersky.msu.ru/visualcmat |
| PDB2Graph [47] | SA (L,W,M) | – | R, F | 2.1 | I / F | 0 / 1 | http://bioinf.modares.ac.ir/software/pdb2graph | |
| STRESS [48] | SA (L, M) | – | R | 2.1 | S / S | 2 / 29 | https://github.com/gersteinlab/STRESS | |
| AlloSigMA [49] | WS | – | R, F, 3D, D | 2.1 | E / E | 13 / 36 | http://allosigma.bii.a-star.edu.sg/home/ | |
| Protein–protein interactions | PPI3D [50] | WS | – | R, F, 3D, D | 2.2 | I / I | 2 / 13 | http://bioinformatics.ibt.lt/ppi3d/ |
| DisruPPI [51] | SA (L) | Interface region | N.A. | 2.2 | N.A. | 0 / 3 | N.A.f | |
| MutaBind [52] | WS | – | R, 3D, D | 3.1 | M / S | 15 / 55 | http://www.ncbi.nlm.nih.gov/projects/mutabind/ | |
| iSEE [53] | SA (L, W, M) | Precomputed datag | R | 3.1 | Ih | 1 / 12 | https://github.com/haddocking/iSee | |
| mCSM-PPI2 [54] | WS | – | R, F, 3D, D | 3.1 | I / M | 1 / 7 | http://biosig.unimelb.edu.au/mcsm_ppi2/ | |
| Protein–nucleic acid interactions | mCSM-NA [55] | WS | – | R, 3D, D | 3.1 | I / I | 5 / 27 | http://biosig.unimelb.edu.au/mcsm_na/prediction |
| PremPDI [56] | WS | – | R, 3D, D | 3.1 | M / S | 0 / 3 | https://lilab.jysw.suda.edu.cn/research/PremPDI/ | |
| Protein–ligand interactions | mCSM-lig [57] | WS | Ligand affinity to wild-type | R, 3D | 3.1 | F / F | 20 / 48 | http://biosig.unimelb.edu.au/mcsm_lig/prediction |
| Ligand transport | CaverDock [58–60] | WS | Starting point of tunnels, ligand | R, F, 3D, D | 2.3 | F / F | 4 / 9 | https://loschmidt.chemi.muni.cz/caverweb/ |
| Dynamics | DynaMut [61] | WS | – | R, F, 3D, D | 3.2 | F / M | 43 / 68 | http://biosig.unimelb.edu.au/dynamut/ |
| Electrostatics | Mutantelec [62] | WS | – | R, F, 3D, D | 3.3 | M / S | 2 / 2 | https://structuralbio.utalca.cl/mutantelec/ |
| AESOP [63] | SA (L, W, M) WS | – | R, F, 3D | 3.3 | I / F | 6 / 6 | https://github.com/BioMoDeL/aesop/, https://aeolus.engr.ucr.edu/aesop/i | |
| Complete pipeline | HotSpot Wizard [64,65] | WS | – | R, F, 3D, D | 4 | F / F | 21 / 60 | https://loschmidt.chemi.muni.cz/hotspotwizard/ |
| Data integration | BioStructMap [66] | SA (L, W, M) WS | – | R, F | 3.4 | I/ F | 0 / 0 | https://github.com/andrewguy/biostructmap, https://biostructmap.burnet.edu.au/i |
aWS, web-server and SA, standalone. For standalone tools, supported operating systems are listed: W, windows; L, linux and M, MacOS.
bAll tools require structural input for the wild type (WT) protein or complex as PDB file or PDB id code, except for PPI3D and HotSpot Wizard, which alternatively can start from a protein sequence only.
cFormats of provided outputs: R, raw data; F, figures; 3D, 3D structure and D, downloadable data.
dApproximate calculation runtimes for small/large proteins: I, instantaneous (≤1 min); F, fast (≤5 min); M, moderate (6–15 min); S, slow (16–60 min); E, extensive (h); for details, see Supplementary Table 1 available online at https: //academic.oup.com/bib.
eUtilization of the tools are represented as the number of citations to the practical use of the tool/the total number of citations; for details, see Supplementary Table 2 available online at https: //academic.oup.com/bib.
fContact authors (cbk@cs.dartmouth.edu).
gInputs comprise the 3D structure of the WT and mutant complexes, eight energy terms, and evolutionary information.
hThe runtime is reported for an example case for which non-trivial input data have already been precomputed.
iWeb-page not accessible at the time of submission; N.A., not available.