**Welcome to Brown Lab** Molecular Modeling and Bioinformatics @ Virginia Tech ============================================================================== ![enter image description here][1] In this OSF, a series of tutorials is provided to get an idea of the language and programs that we commonly use in our lab. The more you work to learn the “how” and “why” of the programs now, the easier it will be when you utilize them for your own research. Understand what the command does and how you can utilize it; do not just type it in and move forward without understanding. This will greatly benefit you in the future. You must complete all tutorials before moving into your own research; however, this does not mean you cannot begin searching the literature about your project and briefly learning more while doing tutorials. These tutorials are provided under the assumption that you are a member of Brown lab and are using a lab computer and/or Virginia Tech resources. HOWEVER, these tutorials are easily adapted to your own environment provided you have downloaded the software and installed some source code as in the instructions provided by them for your local environment. For example, most of these tutorials can be done remotely, on your personal computer, but will require download and installation, which is not always described here. We are not responsible for your ability to download other open-source programs. Finally, most tutorials are written under the assumption that these programs will be run using Unix/Linux. With some small tweaking of syntax, you will be able to use any operating system for these tutorials. As always, contact Dr. Brown (ambrown7@vt.edu) or Jonathan Briganti (jonbrig@vt.edu) if you run into any issues or need assistance. Want to know even more about our research? Click on the Files button to see our usage files for GROMACS simulations and install instructions. We also have details on how we do docking on that page, some helpful papers, as well as a demo page for our PPAR project. Like how we organize things? Feel free to use this format for your own research projects and collaborations. Feel free to ask us any questions, we want work towards making our science more open and transparent. Happy Researching! Unix/Linux tutorial ------------------- [Learn More][2] > Linux/Unix commands are essential for operating command lines in several applications used in molecular modeling and for navigating supercomputers. ---------- VMD tutorial ------------ [Learn More][3] > VMD is a molecular modeling software that is useful to know, even though it lacks some features that PyMOL has. ---------- PyMOL tutorial -------------- [Learn More][4] > PyMOL is the most commonly used molecular modeling program used in laboratory. Complete the introduction assignment by clicking the link above and see the [PyMOL page][5] for more tutorials. ---------- GROMACS tutorial ---------------- [Learn More][6] > GROMACS is a tool used to run molecular dynamics (MD) simulations. Even if you are not currently performing MD, GROMACS is still useful to learn. Literature Search ----------------- > - Begin a literature search on your research topic. Pubmed is the > best place to start. Ensure that you know how to use the library > resources to access papers if needed (ask if you do not). > > - Find a lot of papers? How do you keep track of them all? Download > EndNote from the VT website (it’s free) on your personal computer. > This will be ESSENTIAL in your paper writing and reference tracking > and makes life 1000x easier. It is much easier to install and learn it > now, rather than later. [1]: https://static1.squarespace.com/static/5ab01d59365f02fdeec78d48/t/5ab01dd4575d1f1af46e993d/1565276985424/?format=1500w [2]: https://osf.io/82n73/wiki/Unix%20%7C%20Linux%20Tutorial/ [3]: https://docs.google.com/document/d/1JELl0fJSpK9fP3TW6nVsv_JGY9a5FRFY-3zOax3DrPQ/edit [4]: https://docs.google.com/document/d/1OyP1ijcs-awV4jbTH_eNHUsOcH2_VQSbPTH2aBqVGTc/edit?usp=share_link [5]: https://osf.io/82n73/wiki/PyMOL/ [6]: https://osf.io/82n73/wiki/GROMACS/