pocketZebra

Web-server For Selection and Classification of Subfamily-Specific Binding Sites by Bioinformatic Analysis Of Diverse Protein Families


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Have a protein family? ...

... to identify and rank binding sites in proteins
by functional significance and select particular positions in the structure
that are important for selective binding of substrates/inhibitors/effectors


OR

Access your results by JobID

JobID:

Example: use ID b6896b1021cfa9 to access example output page
or see Examples section for more

Manage Java security issues with the interactive 3D structure viewer



Security New
This site supports HTTPS protocol. Switch to https now to encrypt your connection.


Contact
Dmitry Suplatov d.a.suplatov at belozersky.msu.ru


Publication
Suplatov D., Kirilin E., Arbatsky M., Takhaveev V., Švedas V. (2014) pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families. Nucl. Acids Res. 42(W1): W344-W349. DOI:dx.doi.org


Acknowledgements
Financial support from Skolkovo Institute of Science and Technology [grant 182-MRA]


Navigation

Questions other people ask about pocketZebra:
Q: HTTPS version?
Q: What is pocketZebra?
Q: Why are the subfamily-specific positions (SSPs) important?
Q: What do I need to run pocketZebra?
Q: Where can I get a multiple sequence alignment for my protein family?
Q: What do I get from pocketZebra?
Q: How can I cite pocketZebra
Q: What is a JobID?
Q: How to skip the "Preprocess" step for large alignments?
Q: I have problems starting the interactive 3D structure viewer at the results page
Q: Still have a question?

Q: Does pocketZebra server support HTTPS connection?
A: Yes, since February 7th, 2017 this site supports HTTPS. Switch to https now to encrypt your connection.

Q: What is pocketZebra?
A: pocketZebra is a new web-server that implements the power of bioinformatics and geometry-based structural approaches to detect and rank binding sites in proteins by their functional significance. Additionally, pocketZebra will identify a list of amino acid residues that are involved in selective binding of ligands. pocketZebra can be used to annotate functional and regulatory sites in protein families and design novel selective inhibitors/effectors. The website is free and open to all users and there is no login requirement.

Q: Why are the subfamily-specific positions (SSPs) important?
A: Proteins within a single family share a common function but differ in more specific properties and can be divided into subfamilies with different specificity, enantioselectivity, stability, etc. Completely conserved positions can define general properties of the entire family (for example, have direct roles in enzyme catalytic machinery) but do not explain functional diversity. On the opposite the subfamily-specific positions (SSPs) – conserved only within protein subfamilies, but different between subfamilies – seem to be responsible for functional diversity (different substrate specificity, catalytic activity, stability, etc.) including selective binding of various substrates. SSPs can contribute to a better understanding of structure-function relationship in proteins and guide the design of novel selective inhibitors/effectors. To learn more about SSPs see our publications.

Q: What do I need to run pocketZebra?
A: A multiple sequence alignment of a functionally diverse protein family and a representative PDB structure of one of the family members.

Q: Where can I get a multiple sequence alignment for my protein family?
A: General biologists that prefer fast automated computations can freely download the corresponding alignment of a protein family from various databases, including PFAM and CATH. Alternatively, for a particular purpose users have an opportunity to build large alignments of protein superfamilies on their own. Consult the following publications as an example: publication1, publication2.

Q: What do I get from pocketZebra?
A: You get a list of binding sites in your protein ranked by functional significance and a list of positions in the structure that are important for selective binding of substrates/inhibitors/effectors. Both on-site and off-line versions of the output are provided.

Q: How can I cite pocketZebra?
A: Please cite

Suplatov D., Kirilin E., Arbatsky M., Takhaveev V., Švedas V. (2014) pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families. Nucl. Acids Res. 42(W1): W344-W349. DOI:10.1093/nar/gku448

Q: What is a JobID?
A: pocketZebra algorithm will be applied to your input data and your results will be placed in a public directory protected by a unique 14-symbol access code (JobID). JobID can be shared with a colleague and used to access your results at any time. You can always delete your results from the public directory by pressing the "Delete job" button at the top of the results page or by sending us an e-mail request containing the JobID.

Q: How to skip the "Preprocess" step for large alignments?
A: The preprocess step makes all pairwise comparisons of sequence in your multiple alignment with the query PDB to find the best match. This step may take some time for very large alignment. In order to skip it you can make the first sequence in the MSA file to be the sequence of your query PDB. If the pdb name is "MyPDB.pdb", then the sequence name in MSA file must be "MyPDB".

Q: I have problems starting the interactive 3D structure viewer at the results page
A: pocketZebra implements JavaScript and Java-based openAstexViewer plugin for on-site visualization of the results. In order to enable this feature you will have to approve execution of the Java plugin - press "Run" (or "Proceed") button when prompted to start the application from http://biokinet.belozersky.msu.ru/ (Windows Example1, Windows Example2, Linux Example).

While pocketZebra output is primarily web-based and viewable on the website, the off-line version of the output is also available. Therefore, if you do not want to use the plugin you can still use pocketZebra and download the results to your computer for off-line use.

Read more about managing typical Java security issues.

Q: Still have a question?
A: Don`t hesitate to contact us.
Contact: Dmitry Suplatov d.a.suplatov at belozersky.msu.ru

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