This is an introductory page for the WAM online modelling facility which details various administrative and legal issues. If you have read this already, you can go straight to the sequence entry section.

Contents

Costs for commercial users
Unusually long runs (important notice)
Data security
Terms and conditions
Confidentiality/non-disclosure agreements

Costs for commercial users

If you are academic (or any other sort of not-for-profit institution), you can use the service for free , but to avoid "hogging" of the service, use is restricted to five sequences a month. If you are a commercial organisation please read here for details of prices and invoicing arrangements.

In order to maximise confidentiality for your model, you will need to fill out a form when your model is complete, send it to us and we will then give you a password for use in downloading the model , together with the username you supply on submitting your sequence (see below).

Note that if you are doing multiple runs, you should fill out the form just once for all runs, and send it in.

WAM runs generally take anything from 2 hours to 2 days. However, occasionally a run may take longer, up to a week. In order to prevent a bottleneck on the server, we may at busy times need to terminate and reschedule any runs anticipated to take longer than a week. We will inform you if that is the case.

We try to ensure confidentiality of your sequence and final coordinates by use of the widely-used Apache-SSL secure server. In addition, we use the system described above, whereby a password, supplied by us upon receipt of the form, is needed for download.

WAM Antibody modelling service: Terms and Conditions

This service is provided by the University of Bath, Department of Biology and Biochemistry on the following conditions:

• The service is provided at the risk of users or customers.
• The University makes no warranties as to merchantability or fitness for purpose of the models provided and all warranties are excluded to the fullest extent possible under the law.
• The University will take all reasonable steps to see that models contain no inaccuracies, but the University shall not be liable for any inaccuracies nor for any losses whatsoever including but not limited to financial or economic losses caused to users or customers of the service.
• The University shall take all reasonable steps to secure the confidentiality of the information provided by users or customers of the service. However the University cannot guarantee confidentiality and shall not be liable for any breach of confidentiality nor for any losses whatsoever including but not limited to financial or economic losses suffered to users or customers of the service and due to any breach of confidentiality for whatsoever reason.
• The University of Bath may use the name of users of the service in its publicity about the WAM modelling service. If you do not wish your name to be included please notify us of this at the time of your application.

Confidentiality / Non-Disclosure Agreements

The University is willing on request to enter into a confidentiality or non-disclosure agreement in respect of information provided by users of the service, if this is necessary to protect potentially patentable material. We try to ensure confidentiality in sequence submission by use of the Apache-SSL secure server, but this cannot be guaranteed. If you are unhappy with the usual, web-based method of submission, we can arrange to model your sequence if you send it to us on disc via courier. If you want to examine our standard confidentiality agreement, it is available here . If this is acceptable, please contact us (specifying your address) and we will forward it to the legal department for signing. They will then send it direct to you.

Now enter your sequence!

Now you can enter your sequence. There are two ways of doing this; the traditional WAM (and AbM) manual-alignment method or Autoalign .

• Traditional (manual) method: This requires that you manually line up your sequence with the known antibody structures by inserting deletions in the CDRs.
• NEW Autoalign: This is a new algorithm which attempts to automatically add deletions to the CDRs based on the positions of certain key residues; it will work provided certain sequence conditions are met.

. If you require any detailed administrative info, to do with confidentiality agreements etc., beyond what is provided here, please contact Professor Tony Rees.

Last updated 22/11/05