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DaliLite

Introduction

DaliLite computes optimal and suboptimal structural alignments between two protein structures. The Dali method optimises a weighted sum of similarities of intramolecular distances. Suboptimal alignments do not overlap the optimal alignment or each other. Suboptimal alignments detected by the program are reported if the Z-score is above 2; they may be of interest if there are internal repeats in either structure.

Official Website
Download Software

How to use this tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:

  • The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
  • In the following steps, the user has the possibility to change the default tool parameters
  • And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Enter Coordinates

First Input Structure

In this form you can directly enter or paste protein structure co-ordinate information in plain text, using the PDB format. Text copied from word processors may contain meta-characters that cause problems.

First Structure File Upload

Upload a file containing protein structure co-ordinate information in PDB format. There is a file size limit of 2MB.

Use chain ID (first structure)

Only use this chain from the first structure

Second Input Structure

In this form you can directly enter or paste protein structure co-ordinate information in plain text, using the PDB format. Text copied from word processors may contain meta-characters that cause problems.

Second Structure File Upload

Upload a file containing protein structure co-ordinate information in PDB format. There is a file size limit of 2MB.

Use chain ID (second structure)

Only use this chain from the second structure

Step 2 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).

References

DaliLite workbench for protein structure comparison.
(2000 June) Bioinformatics (Oxford, England) 16 (6) :566-7
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 July 01) Nucleic acids research 43 (W1) :W580-4
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 July) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 July) Nucleic acids research 41 (Web Server issue) :W597-600