Zebra2

A more advanced and easier-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies







... to identify and prioritize subfamily-specific and conserved positions in a functionally diverse superfamily and to select hot-spots for rational design of the query protein


Version 2.0 since November 20th, 2019




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Highlights:

  • The Zebra2 (i.e., Zebra v.2) is a new highly automated on-line tool to identify conserved positions that provide general properties shared by all homologs in the superfamily, and to reveal specific positions responsible for functional diversity within a common structural fold;

  • Information about both conserved and specific positions can help to understand how the enzyme performs its natural function, while the latter can also be selected as hotspots for directed evolution or rational design experiments in an attempt to improve the wild-type protein variant for a particular purpose;

  • The bioinformatic analysis is supported by the integrated Mustguseal web-server to construct large structure-guided sequence alignments of functionally diverse families that can include thousands of proteins based on all available information in public databases;

  • The Zebra2 results are automatically prioritized by the bioinformatic analysis and provided at four information levels to facilitate the knowledge-driven expert selection of the most promising positions on-line: as a sequence similarity network, interfaces to sequence-based and 3D-structure-based analysis of conservation and variability, and accompanied by the detailed annotation of proteins accumulated from the integrated databases with links to the external resources (i.e., PDB, Uniprot, BacDive, BRENDA);

  • The integration of web-based bioinformatic tools Zebra2 and Mustguseal provides an out-of-the-box easy-to-use solution, first of its kind, to conduct a systematic analysis of homologous proteins to study common and specific patterns of local structure associated with a function, select hot-spots for rational design and prepare focused libraries for directed evolution.




Publication: D. Suplatov, Y. Sharapova, E. Geraseva, V. Švedas (2020) Zebra2: a more advanced and easier-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies. submitted




Navigation:





Usability:
  • The Zebra2 input and output can be created, processed and studied entirely on-line via the web-interface. The only software required on the user side is an HTML5-compatible web-browser. Connection via the HTTPS protocol is advertised as default. Optional security features available: IP-/password-based authentication, “Delete” function;

  • The Zebra2 web-server is integrated with the Mustguseal web-server to automatically collect and align a large representative set of proteins within a superfamily with high structural, but low sequence similarity to the query protein of interest. Press the button to automatically construct a large multiple alignment by Mustguseal based on the PDB structure of your query protein to be further processed by the Zebra2;

  • Press the button and then press the Demo mode button to request a demonstration of the Zebra2 web-server;





Contacts and support

Dmitry Suplatov






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