Mission

HOPE is developed at the Centre for Molecular and Biomolecular Informatics CMBI at Radboud University in Nijmegen.

Our mission is to build an automatic mutant analysis server that can provide insight into the structural effects of a mutation. HOPE is aimed at users in the (bio)medical field who wish to visualize and understand their mutation of interest. We hope that these new insights can be used directly in a publication and/or for intelligent design of further experiments. The fact that a 3D analysis of a mutated protein structure can contribute to a wide range of research fields is underlined by earlier projects in which the structural analysis was performed manually.

Method

HOPE goes through a complex process to analyse the mutant of interest. More information about this process can be found on the method page.

We tested Project HOPE by running a number of previously analyzed cases. We compared HOPE's results with the results of our manual analysis and with the results of the well-know PolyPhen and SIFT methods. A page with a summary of these results can be found on here.

Citing HOPE

Please use the following citation when referencing the results in your report:

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces.

BMC Bioinformatics. 2010 Nov 8;11(1):548. DOI: 10.1186/1471-2105-11-548. PubMed: 21059217.

Informal Notice

Please express your gratitude for this free material by citing the above article.

The material provided is complete, correct to the best of our knowledge, and holds all that is needed to start building your own HOPE server. If you do so, please provide a link to the HOPE server. If you want to get a flying start by getting access to the HOPE decision tree, feel free to contact us.

Privacy

This section outlines the ways in which the HOPE website handles information about users. This should not be read as a legal document, but as a description of how we handle information that could be considered sensitive.

Sensitive Data

HOPE saves your input data for anyone to access. This means that the protein and mutant you enter are stored in a server-side report for later use. Any other user, who enters the same data, can access this report later on.

HOPE also stores your IP address when you submit a query, but this is accessible for the administrator only.

Personalized tracking

HOPE uses Google Analytics(GA) to help us analyze how users navigate the various site-pages. GA uses a single-pixel "web bug" image, which is served from every page, a javascript script that collects information about each request, and cookies that maintain information about your usage of the site between visits. For more information of how traffic is analysed, read the description on the GA website.

We use the information generated by GA purely to assess the usefulness and popularity of different features of the site. We have configured GA to not provide the ability to track individual users' usage of the site. However, GA does provides a high-level anonymized overview of the traffic that passes through the site, including such information as the approximate geographical location of users, how often and for how long they visited the site, etc.

We will never (and will not allow any third party to) use the information by the GA to track or to collect any Personally Identifiable Information of visitors to our site. Neither will we will link, or seek to link, an IP address with the identity of a computer user.

If you have any concerns about our use of Google analytics, please feel free to contact us.