Frequently Asked Questions

We have organised the FAQs into sections and we hope to extend this list depending on your feedback. You may also find the forum a useful place to find answers to your questions.

End of Find-a-Drug

When will Find-a-Drug end?
The entire project ends on 16 December 2005.

We are obviously very grateful for the contributions of members and will continue to work with our collaborators.


Will the software be automatically uninstalled?
We have tested an automatical uninstall procedure which we plan to make available.
Why is Find-a-Drug ending?
We have processed more than the 250 queries we originally envisaged. We have also targetted most of the recognised protein targets for the major project areas. Where we have been able to obtain experimental data to confirm biological activity, the predictions have exceeded our expectations.

We have concluded that there are insufficient worthwhile protein queries to continue the project into 2006 and have decided to close the project on 16 December 2005. We will continue to make some new queries available over the coming weeks but will not accept results after the close of the project.


Will the forum be available after the project ends?
We see no reason to close it on the 16 December but we do not envisage it to remain available for weeks. Thereafter we will use a notice page at all the usual website addresses.
Is the decision to close Find-a-Drug financial?
No.
Couldn't you process more molecules for existing queries?
The minimum number of molecules we screen (40 million) is already more than 10x the number routinely screened by typical major pharmaceutical companies. Only for carefully selected queries where we have reason to believe that the additional results will be used have we increased the number of molecules screened.
What is happening with the results to date?
We will continue to work with existing partners as well as seek additional collaborations.
How I can find out about progress in the future?
We will handle news of progress on a case by case basis. Any major announcements will be picked by the Distributing Computing news sites.

Peer to Peer Computing

What is Peer or Peer Computing?
Sometimes known as Distributed Computing, Peer to Peer Computing harnesses the power of a network of computers to perform some computations. For Find-a-Drug and similar internet projects, the computational programs run in background or as a screen-saver application so that they do not significantly intrude on the normal use of the computer.
Can any project be adapted for Peer to Peer Computing?
No. The project has to be divided into a large number of independent calculations which can be distributed to members computers and the results returned to the server(s).
What other aspects are important for such projects?
There are practical restrictions concerning the amount of data that may be distributed and the communication frequency with the server(s). This in turn impacts the choice of algorithms and the number of members a server can support.
How many servers are used by Find-a-Drug?
Unlike some similar projects, we are currently using six in different locations and envisage this number to grow as the number of members also grows. This avoids contention for access to the server as well as redundancy in the event of a network or server failure.
Where can I learn more about distributed computing?
Two relevant web-sites are Internet-based Distributed Computing Projects and Intel Philanthropic peer-to-peer program both of which also provide information about other projects..

Configuration and Setup Issues

I have downloaded and configured THINK but my old screen saver appears
Members must manually configure THINK as their screen saver after they have selected that mode within the Find-a-Drug control panel. Open the Control Panel from the Settings menu (for most versions of Windows) and click on the Display tool in the Control Panel. Click the Screen Saver tab and select THINK from the screen saver chooser. If you wish, you may adjust the delay before clicking the Apply button.
Can I run THINK in background?
Use the visibility controls available from the THINK icon in the System tray or permanently change the setting in the Find-a-Drug control panel (fadsetup.exe).
Can I change the priority of THINK?
The THINK computational thread runs at low priority. You can set the environmental variable THINK_PRIORITY to one of the following values.
ValuePriority
IDLE:IDLE1
IDLE:LOWEST2
IDLE:BELOW_NORMAL3
IDLE:NORMAL4
IDLE:ABOVE_NORMAL5
IDLE:HIGHEST6
 
LOW:IDLE6
LOW:LOWEST7
LOW:BELOW_NORMAL8
LOW:NORMAL9
LOW:ABOVE_NORMAL10
LOW:HIGHEST11
 
BELOW_NORMAL:IDLE11
BELOW_NORMAL:LOWEST12
BELOW_NORMAL:BELOW_NORMAL13
BELOW_NORMAL:NORMAL14
BELOW_NORMAL:ABOVE_NORMAL15
BELOW_NORMAL:HIGHEST16
 
NORMAL:IDLE16
NORMAL:LOWEST17
NORMAL:BELOW_NORMAL18
NORMAL:NORMAL19
NORMAL:ABOVE_NORMAL20
NORMAL:HIGHEST21

Lower priority processes yield to higher priority processes which have more time. The names are derived from the Microsoft windows process class and process priorities and the numbers used directly by the Linux setpriority system routine.

Members can edit think.env using a text editor such as notepad (not word) to set an environment variable by inserting a line such as
THINK_PRIORITY=IDLE:NORMAL


I would like the minimise button to hide the window?
You can reconfigure this button by inserting the line THINK_MINIMIZE=OFF into think.env using a text editor such as notepad.
I am having problems video drivers. Can I disable OpenGL graphics?
Yes under Options in the Find-a-Drug control panel. This should occur automatically if an OpenGL problem causes THINK to crash on startup.
How can I abort the current THINK job?
Make the job queue visible either using the view menu on the THINK window or the THINK icon in the system tray. Then click on the job using the right mouse key and cancel it. If you disable THINK (using the Find-a-Drug control panel) or just stop THINK, then when restarted THINK will continue with the same job.
How can I temporarily suspend the current THINK job?
The THINK icon in the system tray has a Snooze button. THINK will restart after 15 minutes.
Can I suspend the current THINK job until I resume it?
The THINK icon in the system tray has a Sleep button. THINK will not restart until you resume it.
What does the disable button in Find-a-Drug Control panel?
This sends a message to THINK to stop. It can only be restarted by pushing the Enable button.
I have multiple accounts on my PC but THINK only runs for one of them
You need to be logged in for a screen saver to run. Each account needs to be set up to run the THINK screen saver by using the Display tool in the Control Panel. In addition, to connect to the Internet the Server process needs to be started. If the account used to install THINK has write access to the All Users startup folder then every-one will run the SERVER and optionally THINK. Otherwise these programs will only autostart for the account which was used to install them. The Find-a-Drug control panel places think.lgo into an appropriate startup folder and the filetype lgo is registered to start the loader application.
What is the country information used for?
This is used as a basis for some of the statistical analysis as well as selecting an appropriate mirror site for some downloads.
My country is not listed. Why not?
The criteria for inclusion was somewhat arbitrary relating to the population, availability of PCs and probability of participation. There may also have been some inadvertent oversights. If you e-mail countries@find-a-drug.org.uk with your Registration number and password, they will add your country.
When downloading a replacement version, it fails to write server.exe
This is probably because the server is already running. You must stop both the server and think prior to downloading a new version (the automatic download takes care of this).

Statistics

What are statistics?
Members contributions are reported and analysed by team and country in the stats. We report the progress of the projects in the project stats pages. These pages analyse for each target the numbers of jobs processed and the corresponding number of molecules, hits and time taken.
What are teams?
Teams are groups of members for whom the numbers of molecules and hits are totalled. Click here for more information about the statistical reports on the calculations and what teams exist.
How can I form my own team?
Each team must have a web-site, a team captain and a name. You need to e-mail this information to teams@find-a-drug.org.uk, who will assign a team ID. If your web-site is a single page plus reasonable graphics, we will host it. Otherwise, it can be hosted by several other organisation free of charge (eg www.freeserve.com). You may also provide an team icon which is displayed on your team stats page.
What is the best measure of a member's contribution?
The time taken per job does vary and in some cases the number of molecules processed is significantly different. Usually jobs which give a large number of hits take significantly longer than those which give only a few. The number of Points or GFlops is usually a better indication.
What are GFLOPS?
GFLOPS is a measure of the processing performed. It is an abbreviation for Giga Floating point OPerationS. This supercedes our POINTS system which was a more abstract measure of performance. For an average CPU (1.2GHz) this will result in approximately 800 GFLOPS per CPU hour. (Each Point corresponds to 8 GFLOPS).

Security and Privacy

What precautions are taken to ensure the security of information sent from my PC?
All information uploaded to Find-a-Drug servers is encrypted and is transferred to computers inaccessible to the public prior to de-encrypting.
Is it conceivable that Find-a-Drug software introduces a virus or other harmful agent on to my computer?
In order to do so it would be necessary for some-one to hack undetected into Treweren Consultant's computers or Find-a-Drug servers. We take the usual precautions to prevent this and recommend that members continue to run virus detection software. In addition, the download files are regularly replaced limiting the consequences of any infection.
What information does Find-a-Drug upload from my PC?
The only information sent to our servers are the calculations results, time and configuration information which you have entered in the Find-a-Drug control panel. We perform no checks on the accuracy of the processor information, country, e-mail address etc.
What happens if I provide am invalid or incorrect e-mail address?
The e-mail address is used to send quarterly newsletters and if you participate in the beta project information about developments. If you join a team you may elect to receive e-mails from the team captain. If your e-mail address is not valid, we have no means of contacting you.
Who else has access to the information I provide?
The information entered in the Find-a-Drug control panel is encrypted prior to being sent to a Find-a-Drug server and is only de-encrypted on Treweren Consultant's computers which cannot be accessed externally. The information is not and will not be disclosed to third parties.

Hardware issues

I have a local network of PCs. Can I run THINK on all of them without installing the software of each PC ?
Yes. Install Find-a-Drug on the PC which you want to connect to the Internet. Share the folder in which the software is installed with write access enabled. For a PC with the name PC121 and the default folder name (find-a-drug), the software can then be configured for each networked PCs using the command \\PC121\find-a-drug\fadsetup.exe.
Can I run using a shared network drive instead of a shared folder?
This is supported in 1.21a and subsequent releases. It continues to be important that the networked PCs have write access but they do not all need to refer to the folder using the same drive letter.
Can THINK use multiple CPU on the same PC?
This will occur by default if you have a multi-processor PC unless you set or restrict the number of copies under Options in the Find-a-Drug control panel.

Attempting to run more copies of THINK than CPUs will generate an error.


Can I run THINK under Windows 95?
The installation under Windows 95 is not currently supported but some members are runnng under Windows 95. If you know about WINSOCK and have it installed (it is required for most distributed computing projects), then the software should run.
What is the minimum specification to run THINK?
A PC with at least 128MB memory, 10 MB of free disk space and an internet connection (such as dial-up).
Will THINK increase the amount of disk space it uses?
Yes. THINK saves locally the protein files (*.pdb) it has downloaded to avoid reloading them unnecessarily in the future. The molecule files (m*.smi) are saved for future use in the cache subfolder. The results files are deleted after use unless there is an error in when they are retained.
Can I run THINK under Linux?
Yes using a command line interface. Graphics are not currently implemented.
Can I run THINK on a Macintosh?
Not at present.

Connection Issues

What are the most common connection problems?
  • Firewall configuration preventing fadsetup and server accessing the Internet
  • Internet Explorer configured for off-line use
  • Proxy configuration issues

Will a fire-wall prevent the Find-a-Drug control panel (fadsetup) and think working normally?
Perhaps. The Find-a-Drug control panel (fadsetup) and the job queue manager (server) use the HTTP to communicate with one of a list of Find-a-Drug servers. You may need to change you fire-wall setup to enable these programs to send and receive data from the servers listed in http.lis and cgi.lis.
The screen saver is reporting that THINK is idle or showing only the Mortar Board hat.
This indicates that more jobs need to be downloaded from a Find-a-Drug server and is normal when the software is first installed for up to 2 minutes.
Despite being idle, no connections are made to the Find-a-Drug server

Check that the server process is running. If not, logout and login and then check again. If this continues to be the case then check that a file named think.lgo is located in an appropriate startup folder and that the filetype lgo is registered to start the THINK loader application (using Windows Explorer click on Folder Options on the Tools menu and then File Types).


The server process is running and attempting to connect to the server, but THINK remains idle
If there are no jobs for any of the projects you have selected this behaviour is to be expected. Check for messages in server.log.
The error message "(10522) Connection failure" is being returned by the Job Queue Server?
When this is being reported during registration and/or the first time the Job Queue Server tries to download jobs, the usual cause is a firewall configuration which prevents fadsetup.exe and/or server.exe access the Find-a-Drug Internet servers. Obviously, if you change the firewall setup later this problem can re-occur. The URLs of the servers are listed in http.lis and cgi.lis.

We have also observed that on some occasions Windows can remember that a server was unavailable when it last tried and give an error without re-trying! Under these circumstances the problem clears if a dial-up Interconnection is restarted, the Job Queue Server restarted or the PC rebooted.


Do you currently support connections through a proxy server?
Under windows the software automatically uses the proxy settings stored for Internet Explorer.

Under Linux you need to insert the following environment variables by editing think.env
THINK_PROXY_HOST=proxy_server
THINK_PROXY_PORT=port
THINK_PROXY_USER=user
THINK_PROXY_PASSWORD=password
The default port is 8080 and is the user or password is unspecified then it is assumed to be blank.


How frequently does THINK connect to the internet?
You can control the frequency of planned connections in the Find-a-Drug control panel. If THINK completes all queued jobs, then an unplanned connection will occur if there are no molecules files from previous protein targets which can be re-used on the current target. If you select "When On-line" then no attempt to dial-up will be made. The "None" setting should be used when you wish to manually download jobs and upload results.
How long does THINK take to complete a job?
This depends on the speed of your computer and how fast it processes each set of molecules against the query. Most average jobs take a few hours on an average PC. The project stats pages provide some analysis of the time taken, number of hits, redundancy etc for each protein target.
Can I disable automatic dial-up to connect to the internet?
Yes, use the Find-a-Drug control panel (fadsetup.exe) and set Planned Connections to "After Confirmation". You can also configure the software to only upload results and download new jobs when the computer is already on-line by using the "When on-line" option under Planned Connections.
I have enabled automatic dial-up but a connection dialog continues to appear
This is the default Windows connection dialog unless your ISP has provided a replacement. The default Windows dialog (for most versions) includes a toggle "Connect Automatically" but for ISP dialogs this is often hidden as a sub-dialog. If you can't find it from the connection dialog, try other dialup networking dialogs.
My PC does not disconnect after connecting to the Find-a-Drug server
The normal Windows dialogs includes a sub-dialog with a "disconnection when idle" option. The exact details of this vary although some include a "low traffic" disconnect rather than "zero traffic" disconnect. This is preferrable because there have been reports of other software polling the internet and retaining the connection. It is believed that the AOL custom dialogs do not include an automatic disconnect feature!
My PC is disconnecting when I leave Outlook Express and prematurely terminating the download from Find-a-Drug
There is an option in Outlook Express (Tools|Options|Connections) to disconnect after sending and receiving e-mails. Disable this option!
How much data is transferred?
This does vary. The minimum downloaded is about 5Kbytes, but when a new protein target is required a further 50Kbytes will be transferred. These quantities are small compared to most other Distributing Computing projects are will normally be transferred in much less than 1 minute.

Projects

How do you select projects?
The most important aspects of a project are to ascertain the scientific feasibility of the project and the value to society.
Who funds Find-a-Drug?
At present, Find-a-Drug is funded by Treweren Consultants (the developers of the THINK software). In the future, we expect some revenue from partners who will fund some of the research and royalties from discoveries.
Who benefits from the projects?
Find-a-Drug operates on a not for profit basis. This means that all revenues (including any royalties from the sales of any resulting drugs) in excess of costs will be donated to research.
Who controls what happens to the results?
When there is an external partner, the partner is responsible for deciding which molecules to make and test.
Can I opt in or out of projects?
Yes, just run the Find-a-Drug control panel (fadsetup.exe) and change the toggles.
Where can I find out more about the projects?
Click here for the Projects pages.

Science

What does the software do?
The Find-a-Drug software downloads a job consisting of a protein target and a set of 100 molecules from the server. When your PC is otherwise idle, it generates about 100 derivatives for each molecule giving a total of 10,100 molecules. The software then generates all the possible shapes or conformations of each molecule and determines whether it can interact favourably with the receptor in the protein target.
What can I see on the screen?
THINK displays the conformation of the molecule it is currently processing and the progress of the calculation through the job. Faster PCs download several jobs at the same time so that the "percentage complete" will rise to 100 and then fall to 0 without connecting to the internet.
What is the significance of the colours of the balls and sticks?
Each ball corresponds to an atom and each stick to a chemical bond between two atoms and these are coloured in accordance with the elements. The common colours are: blue for nitrogen, red for oxygen, yellow for sulphur and cyan for carbon.
What is the significance of the Mortar Board or academic hat?
This is the THINK logo and it is displayed when THINK is not generating conformers for a molecule - THINK may be generating derivatives or waiting for data.
How many conformers (or conformations) does a molecule have?
This varies from tens to potentially millions of shapes. However, these are grouped into similar sets in such a way that when one conformer is rejected many more may also be rejected at the same time as the program progresses to a different shape.
What is a hit?
This is a molecule which is predicted to interact or bind with the protein receptor.
How do you distinguish a good hit from a poor hit?
The hits are scored in such a way that those which score less than 0 are predicted to bind to the protein receptor. Good inhibitors often have a score less than -50 whereas molecules with scores above -25 can only be expected to bind weakly.
How many molecules are there in each job?
This may change for different protein targets, but normally each job considers 10,100 molecules - 100 are downloaded from the server and 100 derivatives of each molecule are then processed.
Where do the molecules come from?
They have been collected from public domain catalogues and combinatorial chemistry libraries of molecules which are either commercially available or readily synthesised.
What is the difference between the version of THINK used for this project and that hosted by United Devices?
We are using the latest release of THINK which is substantially faster (in part as a result of assistance provided by Intel) and refines all the crude hits at the same time. This has the consequence of lowering the apparent hit rate because only the best hits are returned to the server. In practice, this has an added benefit: the internet data traffic is significantly reduced.
Where can I find out more information about THINK?
THINK is developed and maintained by Treweren Consultants

Results

Who owns the IPR in the results?
Members waive any Intellectual Property Rights (IPR) in the results in the licence agreement. The computational predictions are confirmed by experiments by Find-a-Drug in partnership with academics or small pharmaceutical companies. A fee is payable to Find-a-Drug to transfer or licence the IPR. This fee may be paid on reaching certain milestones in the drug development process or can take the form of royalties on sales.
Who is funding this project?
Find-a-Drug operating costs are presently being paid by Treweren Consultants. This has no bearing on ownership or exploitation of the results.
What happens to the profits?
The Find-a-Drug trustees will distribute any profits to research. As the costs of running the project are low, this would include a substantial part of any royalties.
Is Find-a-Drug a charity?
We are seeking charitable status for Find-a-Drug although it is likely to be some months before this is approved. Being a charity would have certain tax advantages once there is some income!
When does Find-a-Drug expect to generate some income?
We expect to enter into some partnership agreements during 2005 which may include an upfront payment to transfer the IPR in the results for certain protein targets. Thereafter Find-a-Drug will be self-funding.
Will the results be published or put in the public domain?
It is normal practice to patent the activity of molecules once this has been confirmed experientally. This serves to place some of the results in the public domain as well as protect the intellectual property.
What about public interest projects?
The results from public interest projects such as the Bioterrorism antidote project are freely available to approved academic and goverment laboratories.
Can academics access the results without charge?
We look sympathetically at requests from academics for a subset of the results as well as suggestions of certain protein targets.