Tops

You can find the server here

Mention that the server is moving to Glasgow, Leeds, respectively.

1.Operation

1.1. User interface, on-line help, choice of parameters and databases
There is a lot of links to web servers somehow connected to Tops diagrams on the tops mainpage. One of them is to Topology based structure comparison. If you open the link, you have three possibilities: you may perform 3D coordinates to database search or 3D to 3D or finally Tops diagram to 3D (interesting is only the first one. On this decision page there is also a link to help and explanation page, which is very important at later stages of search. It is good to read in advance. There is a lot of links to web servers somehow connected to Tops diagrams on the tops mainpage. One of them is to Topology based structure comparison. If you open the link, you have three possibilities: you may perform 3D coordinates to database search or 3D to 3D or finally Tops diagram to 3D (interesting is only the first one. On this decision page there is also a link to help and explanation page, which is very important at later stages of search. It is good to read in advance. One might choose how many hits will be reprted to her/him.
1.2.Interactive versus E-mail results or notification
The upload of the file is interactive, but the results are send by email
1.3. Documentation, access to literature references
There is link on the main page to page with references.
1.4. Confidentality
No information found
1.5. Elapsed time between submission and results
Very fast, usually no longer than three minutes
1.6. How long are the results kept on the server ?
email only

2. Presentation of results

2.1. What information is reported for the hits?
The list of hits contain three things: PDB ID of matched structure, its CATH code and score. As an options you might want residue matches and pattern generation. The list is very long.
2.2. Measure(s) for goodness-of-fit and statistical significance?
some sort of score (score between 0-10 should be significant), but no explanation, what the score really means.
2.3. Structure-based sequence alignment?
No (but you can get residue matches between structures)
2.4. PDB files with superimposed structures?
No
2.5. Interface with visualization software?
No
2.6. Hyperlinks to the other web-based resources (e.g., PDB)
Not from the results

3. Implementation issues

3.1. Are there parameters the user can set to optimise the results?
No
3.2. Is there a choice of database? How much of the structural universe do they cover?
You can choose among:
- Tops atlas (3567 domains)
- CATH list of non-identical representatives v. 2.4(6839 domains)
- SCOP PDB90 (3033 domains)
- entire PDB as of Feb 2000 (35569 domains)
Cath has been disconnected from the server, therefore we used SCOP database for dehalogenase, ribonukleotide reductase, vitteline, Pnp oxidase, grea and PCNA folds.
3.3. How often are the databases updated?
No specific information about database update.

Note: The server can, in principle, accept also multi-domain proteins, but their splitting into domains is strongly encouraged. Better results with beta strands than alfa helices.

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