PLOP is freely available for academic purposes. Currently, we provide executables for Linux; executables for other platforms may be available in the future. There is no single paper describing the program at present, but several papers have been published on the individual algorithms (side chain, loop, helix sampling, ligand scoring, induced fit, etc.); please cite whichever ones are relevant to the use you are making of the program.
Please keep in mind that the program is constantly being updated. It's entirely possible that two versions of the code will give somewhat different results, as we attempt to improve the algorithms. Bugs may creep in, and we do want to know about them. Please, if you wish to report a bug, send me the log file and any input files, so I can try to figure out what's going on. We are attempting to create a comprehensive manual, but it's a constant struggle to keep it up to date, so please be patient and ask if you have questions.
The following information describes how to obtain a license. If you have any questions about this procedure, please contact Darya Bubman (firstname.lastname@example.org; 415-237-1585).
IMPORTANT: The academic license is a site license. A number of academic institutions have already signed licenses which may cover your use. Please inquire with Darya Bubman. If this is the case, then you will be asked to read the terms of the license and acknowledge them, but you will not need to obtain a signature from an authorized representative of your institution.
Print two copies of the software license and have them filled out (first blank should include a date, second blank should include the name of your institution, third blank should include the official address of your institution) and signed by an authorized representative of your institution (this individual will usually reside in your institution's licensing/technology transfer office and must be authorized to sign license agreements on behalf of your institution; most researchers, including department chairs, are NOT authorized representatives). Please email a copy to the UCSF Office of Innovation, Technology & Alliances, Darya Bubman, PhD, email@example.com. If your institution requires hard copies of the fully executed license, then send both paper copies to Darya Bubman's attention at the UCSF Office of Innovation, Technology & Alliances, 3333 California Street, Suite S-11, San Francisco, CA 94143-1209, so that she can return a fully executed original to your institution. Be sure to include your contact information when you send over the license, as well as the contact information for the individual to whom one fully executed license should be returned. We then will send you the software.