VENUS | This web app | http://venus.cmd.ox.ac.uk/ | Ferla MP, Pagnamenta AT, Koukouflis L, Taylor JC, Marsden BD. (2022). Venus: Elucidating the Impact of Amino Acid Variants on Protein Function Beyond Structure Destabilisation. J Mol Biol. 434(11):167567. https://doi.org/10.1016/j.jmb.2022.167567 |
Michelaɴɢʟo | Results can be exported to Michelaɴɢʟo, edited and shared | http://michelanglo.sgc.ox.ac.uk/ | Ferla, M. P., Pagnamenta, A. T., Damerell, D., Taylor, J. C., & Marsden, B. D. (2020). MichelaNglo: Sculpting protein views on web pages without coding. Bioinformatics, 36(10), 3268–3270.https://doi.org/10.1093/bioinformatics/btaa104 |
Uniprot | Uniprot collates feature information. Within the entry for the protein are many useful pieces of information, including references. | https://www.uniprot.org/uniprot/ | Bateman, A., Martin, M. J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bursteinas, B., Bye-A-Jee, H., Coetzee, R., Cukura, A., Silva, A. Da, Denny, P., Dogan, T., Ebenezer, T. G., Fan, J., Castro, L. G., … Zhang, J. (2021). UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489.https://doi.org/10.1093/nar/gkaa1100 |
gnomAD | gnomAD provides information of variants in the human population. Within the site, the data can be filtered into controls only and allele frequency and zygosity can be found. | https://gnomad.broadinstitute.org/ | Karczewski, K. J., Francioli, L. C., Tiao, G., Cummings, B. B., Alföldi, J., Wang, Q., Collins, R. L., Laricchia, K. M., Ganna, A., Birnbaum, D. P., Gauthier, L. D., Brand, H., Solomonson, M., Watts, N. A., Rhodes, D., Singer-Berk, M., England, E. M., Seaby, E. G., Kosmicki, J. A., … MacArthur, D. G. (2020). The mutational constraint spectrum quantified from variation in 141,456 humans. Nature, 581(7809), 434–443.https://doi.org/10.1038/s41586-020-2308-7 |
PDB | VENUS automatically chooses the model for the user. But this may not be the most interesting | https://www.rcsb.org/ | Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Christie, C. H., Dalenberg, K., Di Costanzo, L., Duarte, J. M., Dutta, S., Feng, Z., Ganesan, S., Goodsell, D. S., Ghosh, S., Green, R. K., Guranovic, V., Guzenko, D., Hudson, B. P., … Zhuravleva, M. (2021). RCSB Protein Data Bank: Powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Research, 49(1), D437–D451.https://doi.org/10.1093/nar/gkaa1038 |
Swiss-Model | If no structures are available, VENUS uses Swiss-Models as these are threaded and may contain oligomers. Other database of models exist, such as ModBase, as do modelling servers, such as Phyre or I-Tasser. | https://swissmodel.expasy.org/ | Bienert, S., Waterhouse, A., De Beer, T. A. P., Tauriello, G., Studer, G., Bordoli, L., & Schwede, T. (2017). The SWISS-MODEL Repository-new features and functionality. Nucleic Acids Research, 45(D1), D313–D319.https://doi.org/10.1093/nar/gkw1132 |
AlphaFold2 | If no suitable model can be found Venus uses the EBI-AlphaFold2 models. | https://swissmodel.expasy.org/ | Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021).https://www.nature.com/articles/s41586-021-03819-2 |
PDB model depositors | The paper associated with a structure (or the homologue used by Swiss-Model or other tools) generally contains a treasure trove of information | — | Context dependent fetched information |
PhosphoSitePlus | PSP is a database collecting post-translational modifications from high throughput screens. | https://www.phosphosite.org/ | Guex, N., Peitsch, M. C., & Schwede, T. (2009). Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. ELECTROPHORESIS, 30(S1), S162–S173.https://doi.org/10.1002/elps.200900140 |
Eukaryotic Linear Motif (ELM) | The ELM database contains a myriad know linear motifs found in eukarytes | https://elm.eu.org/ | Kumar, M., Gouw, M., Michael, S., Sámano-Sánchez, H., Pancsa, R., Glavina, J., Diakogianni, A., Valverde, J. A., Bukirova, D., Signalyševa, J., Palopoli, N., Davey, N. E., Chemes, L. B., & Gibson, T. J. (2020). ELM-the eukaryotic linear motif resource in 2020. Nucleic Acids Research, 48(D1), D296–D306.https://doi.org/10.1093/nar/gkz1030 |
ConSurf‐DB | The ConSurf‐DB was used to get conservation profiles | https://consurfdb.tau.ac.il/ | Ben Chorin A, Masrati G, Kessel A, Narunsky A, Sprinzak J, Lahav S, Ashkenazy H, Ben-Tal N. ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins. Protein Sci. 2020 Jan;29(1):258-267.https://doi.org/10.1002/pro.3779 |