With the development of time, Rosetta has become more and more powerful, covering more and more fields, and more and more concerned users. But Rosetta may be difficult for some newcomers to get started. Therefore, this article hopes to answer some of the most concerned questions of users who are new to Rosetta in the form of FAQs, and help everyone to get started quickly.
Rosetta is a polymer modeling software library based on Monte Carlo simulated annealing as the core of the algorithm. It is written in C++ code (also written in python). Use Rosetta's built-in scoring function and various methods to sample biological processes, evaluate and optimize these polymer structures, and output the required results. Rosetta generally supports the calculation of proteins, nucleic acids and small chemical molecules, as follows：
✓ Protein–Protein Docking
✓ Protein–Peptide Docking
✓ Protein–Ligand Docking
✓ Protein Design
✓ Protein Loop Modeling
✓ Nucleic Acids modeling
✓ Solving Crystal Structures
✓ Solving NMR structures
Rosetta can now be understood as a "program library" for biomolecular modeling, in which functions can be disassembled or independent. The functional modules in Rosetta can be used in many ways:
✓ After installing and compiling Rosetta source code, use the command line to call Rosetta applications
✓ After installing the PyRosetta package, call it through a Python script (advanced)
✓ By writing RosettaScripts, you can customize the calculation method flow required by the user to achieve a specific purpose (advanced)
✓ Rosetta also has some GUI interfaces, such as PyRosetta Toolkit, Foldit, etc.
✓ Online server, the Rosetta team provides academic free online servers, such as ROSIE, etc., server preview list
✓ Usually for novice online server and compiling and installing methods are the most common methods of use.
There are many free Linux distributions. Generally speaking, Rosetta will be compiled and tested under Ubuntu and CentOS7 (Message from Sergey Lyskov) before release. Therefore, when choosing a system, these two releases should be selected first. Compared with the rapid update iteration of Ubuntu, the development environment of CentOS7 is more stable. For the friendliness of newcomers, I personally recommend compiling under ubuntu.
Rosetta is not a traditional exe application. We can't double-click the icon to complete the installation like in windows. There are two main ways to install Rosetta, one is to compile and install itself through the source code, and the other is to directly download the pre-compiled version of Rosetta (including the source code). For beginners, I recommend downloading the pre-compiled version directly (the disadvantage is that the download package is relatively large, about ~7GB) and setting the required environment correctly. In the future, friends who have a certain understanding of Linux can choose to compile and install by themselves.
✓ You can try to post in the RosettaCommon forum for help, but this forum requires registration with an academic mailbox.
✓ You can also send an email directly to the developer. If it is determined that it is a bug in the program, please report it to the developer immediately.