Hello,
I am currently trying to evaluate whether our group should purchase licenses for the YASARA suite. I have downloaded the free YASARA view software and it's quite nice and user friendly as advertised. This will definitely become one of the tools that I will use to look at structures in certain circumstances. But what I am interested in is whether the additional features that one has to pay for are necessarily useful.
I realize there are molecular modelling, docking and simulation packages. The autoSMILES script looks nice as well. The whole thing seems a bit black box and the videos and the small teasers on the website make it sound like everything is just done with a click. I'm not sure if that's a good thing or not. Currently, we use a number of modelling servers to build models, use AutoDockTools to prepare docking runs for AD4 and ADvina and use the GROMACS and AMBER suites for MD, utilizing antechamber for small molecule parameterization. So we do have alternatives for almost all of the features of the YASARA package.
As I have never used the program before I was wondering if those who have used it the software could give me some insights into the usefulness and whether the researcher can actually fine-tune the parameters of all the features. Also if you could point me towards any literature concerning the YASARA package or some good literature that utilized the package, I would be very grateful.
Thank you.
Yasara is a good software without any doubt. However, some other equally good software suites are Discovery Suite, Schrodinger Suite. So, I believe you can have a look for their features as well and then decide. In terms of QSAR Schrodinger ranks higher than any other softwares. In terms of visualization VMD has a very good graphics and PyMol as usual is very friendly. In case of docking Discovery Studio Suite is very easy to do. For protein-protein interaction Schrodinger is very good and the results are reliable. Also, you can go through some of the publications which would give you better understanding. Hope the answer is useful.
I am using mostly YASARA for molecular modeling and some simulation experiments. Actually it is quite user friendly, as you perform everything with predefined macros. You only need to prepare a scene with your structure, your substrate or ligand and then you run the macro. It is very easy to use with the predefined macros. Most of them, have a first part that explain what the command does, and how you can change; this way you can easily change parameters interesting for proteins as ionic strength, pH and temperature. If you are more into informatics, you can fully parametrize the macro, by altering also the part of it which is not described in detail (for instance you can exchange your solvent from water to any solvent that you want, if you know how to alter the macro). Unfortunately, I think that the documentation of YASARA is not sufficient to help you develop on this topic, if you are not experienced enough.
Another interesting feature of YASARA is that it has the AMBER force fields included, but they also developed their own. You can find the citations to them from their site.
Before you purchase it, maybe you can check the Fold X (free) plug-in for YASARA, for a short evaluation. You can learn more about its features in the provided link (there is also a publication explaining all its features).
Just for your information, for visualization I prefer to use PyMol.
http://foldxyasara.switchlab.org
user friendly,charm but the support is very poor,i contacted them many times,NO REPLY AT ALL!!
manual which is not enough,
for charmm, you can go to charmm forum the support their is good. I have asked many times and get good responses.
YASARA is my favorite molecular modeling suite. It is user-friendly yet extremely powerful and fast. The licensing is relatively inexpensive and flexible. The more I use it, the more I appreciate it.
I am not sure, but it seems reasonable that you would need to have a license to get technical support. I have a group leader license, and I have always received a reply to my technical questions about YASARA software. It might take a few weeks, but the answer comes.
One should remember that YASARA is not a big company with a tech support team -- it is managed by one person who created the software. Nevertheless, I find that it is as full-featured as molecular modeling suites produced by major corporations. It is also highly intuitive and accurate.
YASARA cannot do everything, but I rely on it for all the things that it can do, and I supplement it with other software for the things it cannot do, such as cheminformatics and QSAR. YASARA's graphics are so good that it has replaced PyMOL as my default molecular viewer.
Pl see the latest version of YASARA and the latest version of FoldX in link
http://foldxyasara.switchlab.org/index.php/Troubleshooting
- Badges
- Science topic