PDB ProtVista: A reusable and open-source sequence feature viewer
Author:
Deshpande MandarORCID, Varadi MihalyORCID, Paysan-Lafosse TyphaineORCID, Nair SreenathORCID, Piovesan DamianoORCID, Mir SaqibORCID, Gutmanas AleksandrasORCID, Tosatto Silvio C. E.ORCID, Velankar SameerORCID
Abstract
AbstractSummaryThe PDB ProtVista is a reusable and customisable sequence feature viewer that provides intuitive and detailed 2D visualisation of residue-level annotations while also supporting interactive communication with 3D viewers. The Protein Data Bank in Europe (PDBe) team develops and maintains PDB ProtVista. Several web services use it to display structural and functional annotations such as macromolecular interaction interfaces, intrinsic disorder predictions, sequence variants, and sequence conservation.Availability and ImplementationThe PDB ProtVista is a native JavaScript (ES6) application that is freely available from https://github.com/PDBeurope/protvista-pdb. The above URL also provides extensive documentation and step-by-step user guides on integrating PDB ProtVista with existing web applications and 3D molecular viewers. It also offers an example of how to display custom data of the user and functional annotations for PDB and UniProt entries powered by a rich set of PDBe API endpoints.
Publisher
Cold Spring Harbor Laboratory
Reference23 articles.
1. Andreeva, A. , Kulesha, E. , Gough, J. , & Murzin, A. G. (2020). The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures. Nucleic Acids Research, 48(D1). https://doi.org/10.1093/nar/gkz1064 2. Armstrong, D. R. , Berrisford, J. M. , Conroy, M. J. , Gutmanas, A. , Anyango, S. , Choudhary, P. , Clark, A. R. , Dana, J. M. , Deshpande, M. , Dunlop, R. , Gane, P. , Gáborová, R. , Gupta, D. , Haslam, P. , Koča, J. , Mak, L. , Mir, S. , Mukhopadhyay, A. , Nadzirin, N. , … Velankar, S. (2019). PDBe: improved findability of macromolecular structure data in the PDB. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz990 3. 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. , da Silva, A. , Denny, P. , Dogan, T. , Ebenezer, T. , Fan, J. , Castro, L. G. , … Teodoro, D. (2021). UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1). https://doi.org/10.1093/nar/gkaa1100 4. Blum, M. , Chang, H.-Y. , Chuguransky, S. , Grego, T. , Kandasaamy, S. , Mitchell, A. , Nuka, G. , Paysan-Lafosse, T. , Qureshi, M. , Raj, S. , Richardson, L. , Salazar, G. A. , Williams, L. , Bork, P. , Bridge, A. , Gough, J. , Haft, D. H. , Letunic, I. , Marchler-Bauer, A. , … Finn, R. D. (2021). The InterPro protein families and domains database: 20 years on. Nucleic Acids Research, 49(D1). https://doi.org/10.1093/nar/gkaa977 5. Cilia, E. , Pancsa, R. , Tompa, P. , Lenaerts, T. , & Vranken, W. F. (2014). The DynaMine webserver: predicting protein dynamics from sequence. Nucleic Acids Research, 42(W1). https://doi.org/10.1093/nar/gku270
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