The structure is colored according to the probability that the split sites are active (blue) and inactive (red).
Residues can be selected via Ctrl+Leftclick (a green sphere will show the selection) which treat the selected residue as the site where the protein is split. The split occurs after the selected residue.
Additionally the two split fragments are shown with two colors (red and blue).
Selected residues can be deselected via Ctrl-Leftclicking anywhere but on a residue. A tooltip will appear when
hovering the mouse over the residue. The residues' chain information is displayed after a colon.
The current camera view can be saved via this button.
The size of the structure window can be resized via this button.
Different groups of split sites can be selected outputting a list of split sites ordered from the highest activity probability to lowest.
The high active probability group encompasses sites with a activity probability of at least 0.75. The high inactive probability encompasses sites with a activity probability of less than 0.25.
The active and inactive groups have all sites that the model would predict to be active (at least 0.5) and inactive (less than 0.5) respectively.
The list can be copied to the clipboard with this button.
When a residue is selected, additional information concerning the conservation,
binding affinity, surface accessibility and secondary structure properties are shown here which are used to calculate the activity probability in the model. It is important to note that
conservation and surface accessibility are given as means of the surrounding residues of the split site, as this was shown to work best for predicting the activity,
so the values do not show single residue values (which can be accessed in the raw files) (*). The split site is considered to be in a secondary structure if both flanking residues of the split site are in
a secondary structure region.
Deselecting residues can be done in the structure view or with this button located at the top of the Data tab.
If multiple files were uploaded via batch upload, the single files can be selected via a dropdown menu.
Zooming out can be done via a double-click on the graph or via this button that appears at the top-left of the graph (if it is zoomed in).
This tab shows the models prediction for each possible split site. There are 4 categories given with 4 colors.
Generally speaking the model predicts split sites with a probability of at least 0.5 to be active and below 0.5 to be inactive. Sites with a probability of at least 0.6 have been shown to
contain the highest ratio of true positives to false positives at the dispense of loosing some true positive split sites. Sites with a probability of less than 0.4 have been shown to
contain the highest ratio of true negatives to false negatives.
This tab shows the logit function, which what the model's prediction is based on. The points are sorted by the lowest prediction to the highest (Meaning the splits are not in order like with the other tabs).
The sequence tab shows the sequence with the activity probability color codes,
residue id's and whether the residue belongs to a secondary structure region (marked with Sec).
The raw data can be downloaded in this tab as a zip file.
The zip contains the output from DSSP, hmmer, muscle and rate4site as well as the pdb file that was generated through pdb2pqr at a pH of 7.
At Int&in, accessible from intein.biologie.uni-freiburg.de, one of our main priorities is the privacy of our visitors. This Privacy Policy document contains types of information that is collected and recorded by Int&in and how we use it.
If you have additional questions or require more information about our Privacy Policy, do not hesitate to contact us.
This Privacy Policy applies only to our online activities and is valid for visitors to our website with regards to the information that they shared and/or collect in Int&in. This policy is not applicable to any information collected offline or via channels other than this website.
Consent
By using our website, you hereby consent to our Privacy Policy and agree to its terms.
Information we collect
The personal information that you are asked to provide, and the reasons why you are asked to provide it, will be made clear to you at the point we ask you to provide your personal information. We collect any documents you upload to our service, which is made accessible through a randomized personalized key. Note that the uploaded content may be accessible to others have access to your personalized key. We regularly delete old documents that exceed 30 days since their upload on our service. We do not store information about who uploaded documents, if the user is not logged into an account at the time of upload, although in some cases such a connection may be found trough current logs and timeframe. If the user is using an account, the uploaded documents will be linked to personal data. Should you upload documents not belonging to you, you are responsible for obtaining consent from the respecive owner(s) and for providing privacy notices should the documents contain identifiable contents. It is your responsibility to process documents not owned by you in accordance with applicable law. If a document is uploaded you confirm to us that you have provided all necessary privacy notices and consents from the respective owner(s). If you contact us directly, we may receive additional information about you such as your name, email address, phone number, the contents of the message and/or attachments you may send us, and any other information you may choose to provide. When you register for an account, we may ask for your contact information, including items such as name, company name, institution, address, email address, and telephone number.
How we use your information
We use the information we collect in various ways, including to:
1) Provide, operate, and maintain our website
2) Improve, personalize, and expand our website
3) Understand and analyze how you use our website
4) Develop new products, services, features, and functionality
5) Communicate with you, to provide you with updates and other information relating to the website
6) Send you emails
7) Find and prevent fraud
Personal data uploaded by you
Whether from a cloud-based hosting service or your device, the content you upload to the Services (data, text, graphic, audio, audio-visual files, etc.) may include personal information. Note that the uploaded content may be accessible to others (depending on your settings). We do not store information about who uploaded content if the user is not logged in, but in some cases it is possible to find such a connection (depending on the state of current logs and timeframe). Such data may include file UUID, client IP, user-agent, and referrer. Please be careful when uploading the content and avoid any unintentional disclosure of personal or sensitive information without the other person's consent. If you process the personal data of End Users or other identifiable individuals in your use of our Services, you are responsible for providing legally adequate privacy notices and obtaining necessary consents for the processing of such data. You represent to us that you have provided all necessary privacy notices and obtained all necessary consents. You are responsible for processing such data in accordance with applicable law. We do not modify your content in any way unless you requested such modification from our Services.
Log Files
Int&in follows a standard procedure of using log files. These files log visitors when they visit websites. All hosting companies do this and a part of hosting services' analytics. The information collected by log files include internet protocol (IP) addresses, browser type, Internet Service Provider (ISP), date and time stamp, referring/exit pages, and possibly the number of clicks. These are not linked to any information that is personally identifiable. The purpose of the information is for analyzing trends, administering the site, tracking users' movement on the website, and gathering demographic information.
Cookies and Web Beacons
Like any other website, Int&in uses 'cookies'. These cookies are only functional cookies, that are needed for the website's login functionality and to remember whether the banner with the cookie information was acknowledged.
Below a complete list of cookies that are set by the website:
CCPA Privacy Rights (Do Not Sell My Personal Information)
Under the CCPA, among other rights, California consumers have the right to:
1) Request that a business that collects a consumer's personal data disclose the categories and specific pieces of personal data that a business has collected about consumers.
2) Request that a business delete any personal data about the consumer that a business has collected.
3) Request that a business that sells a consumer's personal data, not sell the consumer's personal data.
If you make a request, we have one month to respond to you. If you would like to exercise any of these rights, please contact us.
GDPR Data Protection Rights
We would like to make sure you are fully aware of all of your data protection rights. Every user is entitled to the following:
1) The right to access - You have the right to request copies of your personal data. We may charge you a small fee for this service.
2) The right to rectification - You have the right to request that we correct any information you believe is inaccurate. You also have the right to request that we complete the information you believe is incomplete.
3) The right to erasure - You have the right to request that we erase your personal data, under certain conditions.
4) The right to restrict processing - You have the right to request that we restrict the processing of your personal data, under certain conditions.
5) The right to object to processing - You have the right to object to our processing of your personal data, under certain conditions.
6) The right to data portability - You have the right to request that we transfer the data that we have collected to another organization, or directly to you, under certain conditions.
If you make a request, we have one month to respond to you. If you would like to exercise any of these rights, please contact us.
Children's Information
Another part of our priority is adding protection for children while using the internet. We encourage parents and guardians to observe, participate in, and/or monitor and guide their online activity. Int&in does not knowingly collect any Personal Identifiable Information from children under the age of 13. If you think that your child provided this kind of information on our website, we strongly encourage you to contact us immediately and we will do our best efforts to promptly remove such information from our records.
Consent
By using our website, you hereby consent to our Privacy Policy and agree to its terms.
Information we collect
The personal information that you are asked to provide, and the reasons why you are asked to provide it, will be made clear to you at the point we ask you to provide your personal information. We collect any documents you upload to our service, which is made accessible through a randomized personalized key. Note that the uploaded content may be accessible to others have access to your personalized key. We regularly delete old documents that exceed 30 days since their upload on our service. We do not store information about who uploaded documents, if the user is not logged into an account at the time of upload, although in some cases such a connection may be found trough current logs and timeframe. If the user is using an account, the uploaded documents will be linked to personal data. Should you upload documents not belonging to you, you are responsible for obtaining consent from the respecive owner(s) and for providing privacy notices should the documents contain identifiable contents. It is your responsibility to process documents not owned by you in accordance with applicable law. If a document is uploaded you confirm to us that you have provided all necessary privacy notices and consents from the respective owner(s). If you contact us directly, we may receive additional information about you such as your name, email address, phone number, the contents of the message and/or attachments you may send us, and any other information you may choose to provide. When you register for an account, we may ask for your contact information, including items such as name, company name, institution, address, email address, and telephone number.
How we use your information
We use the information we collect in various ways, including to:
1) Provide, operate, and maintain our website
2) Improve, personalize, and expand our website
3) Understand and analyze how you use our website
4) Develop new products, services, features, and functionality
5) Communicate with you, to provide you with updates and other information relating to the website
6) Send you emails
7) Find and prevent fraud
Personal data uploaded by you
Whether from a cloud-based hosting service or your device, the content you upload to the Services (data, text, graphic, audio, audio-visual files, etc.) may include personal information. Note that the uploaded content may be accessible to others (depending on your settings). We do not store information about who uploaded content if the user is not logged in, but in some cases it is possible to find such a connection (depending on the state of current logs and timeframe). Such data may include file UUID, client IP, user-agent, and referrer. Please be careful when uploading the content and avoid any unintentional disclosure of personal or sensitive information without the other person's consent. If you process the personal data of End Users or other identifiable individuals in your use of our Services, you are responsible for providing legally adequate privacy notices and obtaining necessary consents for the processing of such data. You represent to us that you have provided all necessary privacy notices and obtained all necessary consents. You are responsible for processing such data in accordance with applicable law. We do not modify your content in any way unless you requested such modification from our Services.
Log Files
Int&in follows a standard procedure of using log files. These files log visitors when they visit websites. All hosting companies do this and a part of hosting services' analytics. The information collected by log files include internet protocol (IP) addresses, browser type, Internet Service Provider (ISP), date and time stamp, referring/exit pages, and possibly the number of clicks. These are not linked to any information that is personally identifiable. The purpose of the information is for analyzing trends, administering the site, tracking users' movement on the website, and gathering demographic information.
Cookies and Web Beacons
Like any other website, Int&in uses 'cookies'. These cookies are only functional cookies, that are needed for the website's login functionality and to remember whether the banner with the cookie information was acknowledged.
Below a complete list of cookies that are set by the website:
| Name | Domain | Purpose | Validity |
|---|---|---|---|
| PHPSESSID | intein.biologie.uni-freiburg.de | Contains a unique string, that is assigned when you open the site, that allows us to keep a user logged in. This is a temporary cookie and is removed when the user logs out or closes the browser window (Some browsers restore the previous session even after closing the browser, the settings can be adjusted in the respective browsers). | Until the Browser is closed |
| hide_banner | intein.biologie.uni-freiburg.de | Hide the cookie information banner | 30 days |
CCPA Privacy Rights (Do Not Sell My Personal Information)
Under the CCPA, among other rights, California consumers have the right to:
1) Request that a business that collects a consumer's personal data disclose the categories and specific pieces of personal data that a business has collected about consumers.
2) Request that a business delete any personal data about the consumer that a business has collected.
3) Request that a business that sells a consumer's personal data, not sell the consumer's personal data.
If you make a request, we have one month to respond to you. If you would like to exercise any of these rights, please contact us.
GDPR Data Protection Rights
We would like to make sure you are fully aware of all of your data protection rights. Every user is entitled to the following:
1) The right to access - You have the right to request copies of your personal data. We may charge you a small fee for this service.
2) The right to rectification - You have the right to request that we correct any information you believe is inaccurate. You also have the right to request that we complete the information you believe is incomplete.
3) The right to erasure - You have the right to request that we erase your personal data, under certain conditions.
4) The right to restrict processing - You have the right to request that we restrict the processing of your personal data, under certain conditions.
5) The right to object to processing - You have the right to object to our processing of your personal data, under certain conditions.
6) The right to data portability - You have the right to request that we transfer the data that we have collected to another organization, or directly to you, under certain conditions.
If you make a request, we have one month to respond to you. If you would like to exercise any of these rights, please contact us.
Children's Information
Another part of our priority is adding protection for children while using the internet. We encourage parents and guardians to observe, participate in, and/or monitor and guide their online activity. Int&in does not knowingly collect any Personal Identifiable Information from children under the age of 13. If you think that your child provided this kind of information on our website, we strongly encourage you to contact us immediately and we will do our best efforts to promptly remove such information from our records.