mdciao.nomenclature

Get and manipulate consensus nomenclature for GPCRs, G-proteins, and Kinases.

Uses local files and/or accesses the following databases and their public APIs

Please see the individual documentation of the Labeler classes for further references and cite them whenever you use these nomenclature schemes in your final publication.

Additionally, use mdciao.nomenclature.references anytime to get more info.

Classes

LabelerConsensus(**kwargs)

Parent class to manage consensus notations.

LabelerGPCR(*args, **kwargs)

Obtain and manipulate GPCR generic residue numbering

LabelerCGN(*args, **kwargs)

Obtain and manipulate G-protein generic residue numbering, i.e. 'Common Gα Numbering', CGN[1] provided by the GPCRdb.

LabelerKLIFS(KLIFS_string[, local_path, ...])

Obtain and manipulate Kinase-Ligand Interaction notation of the 85 pocket-residues of kinases.

AlignerConsensus(maps[, tops])

Use consensus labels for multiple sequence alignment.

Literature()

Quick access to some of the references used by nomenclature

Functions

guess_by_nomenclature

Guess which fragments of a topology best align with a consensus nomenclature.

matching_fragments

Return fragments of the topology that match the reference sequence of LabelerConsensus object

references

Print out references relevant to this module

conlabs2confrags

Subdomain definitions form a list of consensus labels.

References

These are some of the references most relevant to this module:

  • GPCRdb and naming schemes therein

  • Kooistra, A. J., Mordalski, S., Pándy-Szekeres, G., Esguerra, M., Mamyrbekov, A., Munk, C., … Gloriam, D. E. (2021). GPCRdb in 2021: Integrating GPCR sequence, structure and function. Nucleic Acids Research, 49(D1), D335–D343. https://doi.org/10.1093/nar/gkaa1080

  • Isberg, V., De Graaf, C., Bortolato, A., Cherezov, V., Katritch, V., Marshall, F. H., … Gloriam, D. E. (2015). Generic GPCR residue numbers - Aligning topology maps while minding the gaps. Trends in Pharmacological Sciences, 36(1), 22–31. https://doi.org/10.1016/j.tips.2014.11.001

  • Isberg, V., Mordalski, S., Munk, C., Rataj, K., Harpsøe, K., Hauser, A. S., … Gloriam, D. E. (2016). GPCRdb: An information system for G protein-coupled receptors. Nucleic Acids Research, 44(D1), D356–D364. https://doi.org/10.1093/nar/gkv1178

  • Further GPCR naming schemes

  • Ballesteros, J. A., & Weinstein, H. (1995). Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. Methods in Neurosciences, 25(C), 366–428. https://doi.org/10.1016/S1043-9471(05)80049-7

  • Wu, H., Wang, C., Gregory, K. J., Han, G. W., Cho, H. P., Xia, Y., … Stevens, R. C. (2014). Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator. Science, 344(6179), 58–64. https://doi.org/10.1126/science.1249489

  • Pin, J. P., Galvez, T., & Prézeau, L. (2003). Evolution, structure, and activation mechanism of family 3/C G-protein-coupled receptors. Pharmacology and Therapeutics, 98(3), 325–354. https://doi.org/10.1016/S0163-7258(03)00038-X

  • Wootten, D., Simms, J., Miller, L. J., Christopoulos, A., & Sexton, P. M. (2013). Polar transmembrane interactions drive formation of ligand-specific and signal pathway-biased family B G protein-coupled receptor conformations. Proceedings of the National Academy of Sciences of the United States of America, 110(13), 5211–5216. https://doi.org/10.1073/pnas.1221585110

  • Oliveira, L., Paiva, A. C. M., & Vriend, G. (1993). A common motif in G-protein-coupled seven transmembrane helix receptors. Journal of Computer-Aided Molecular Design, 7(6), 649–658. https://doi.org/10.1007/BF00125323

  • Schwartz, T. W., Gether, U., Schambye, H. T., & Hjorth, S. A. (1995). Molecular mechanism of action of non-peptide ligands for peptide receptors. Current Pharmaceutical Design, 1, 325–342.

  • Schwartz, T. W. (1994). Locating ligand-binding sites in 7tm receptors by protein engineering. Current Opinion in Biotechnology, 5(4), 434–444. https://doi.org/10.1016/0958-1669(94)90054-X

  • Baldwin, J. M. (1993). The probable arrangement of the helices in G protein-coupled receptors. The EMBO Journal, 12(4), 1693–1703. https://doi.org/10.1002/J.1460-2075.1993.TB05814.X

  • Baldwin, J. M., Schertler, G. F. X., & Unger, V. M. (1997). An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. Journal of Molecular Biology, 272(1), 144–164. https://doi.org/10.1006/jmbi.1997.1240

  • CGN naming scheme

  • Flock, T., Ravarani, C. N. J., Sun, D., Venkatakrishnan, A. J., Kayikci, M., Tate, C. G., … Babu, M. M. (2015). Universal allosteric mechanism for Gα activation by GPCRs. Nature 2015 524:7564, 524(7564), 173–179. https://doi.org/10.1038/nature14663

  • KLIFS 85 ligand binding site residues of kinases

  • Van Linden, O. P. J., Kooistra, A. J., Leurs, R., De Esch, I. J. P., & De Graaf, C. (2014). KLIFS: A knowledge-based structural database to navigate kinase-ligand interaction space. Journal of Medicinal Chemistry, 57(2), 249–277. https://doi.org/10.1021/JM400378W

  • Kooistra, A. J., Kanev, G. K., Van Linden, O. P. J., Leurs, R., De Esch, I. J. P., & De Graaf, C. (2016). KLIFS: a structural kinase-ligand interaction database. Nucleic Acids Research, 44(D1), D365–D371. https://doi.org/10.1093/NAR/GKV1082

  • Kanev, G. K., de Graaf, C., Westerman, B. A., de Esch, I. J. P., & Kooistra, A. J. (2021). KLIFS: an overhaul after the first 5 years of supporting kinase research. Nucleic Acids Research, 49(D1), D562–D569. https://doi.org/10.1093/NAR/GKAA895

  • PDB

  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000, January 1). The Protein Data Bank. Nucleic Acids Research. Oxford Academic. https://doi.org/10.1093/nar/28.1.235

  • UniProt

  • Bateman, A., Martin, M. J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., … Zhang, J. (2021). UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489. https://doi.org/10.1093/NAR/GKAA1100