Can anybody please suggest what the status of the MOE software package is? How reliable is it in Pharmacophore modeling, QSAR and docking studies?
MOE is written in this high-level language, which has had much simple chemistry built into it. In MOE compiler is proprietary, but all the code is in the public domain, and 95 per cent of it is written in SVL and can be modified easily by user. and you can ask MOE to code algorithms as u need, if ur a commercial user. Coming to reliability, MOE has its own integrated database for modelling, pharmacophore search and its elucidation, it updates with the released version. I Modeled P-Glycoprotein and docking studies in MOE, i felt comfortable and with good output. It has dedicated database for GPCR's, Kinase for modelling them.
In pharmacophore modeling use a generalized ligand representation and geometric constraints to bypass the structural or chemical class bias of 2D methods. QSAR models are built using linear, probabilistic and decision-tree methodologies. You can go ahead when you know MOE customization. All the best..!
hi Venkat Addala, thank you very much for your concern. I would like to know which package is the best among Schrodinger, MOE and SYBYL for docking, pharmacophore modeling (structure/ligand-based) and QSAR studies. I have read a review online about docking in MOE and it wasn't very positive. If I go for good publication using MOE, what is the status???
Hi I think sybyl is the best among the software you mention. Though Schrodinger is also good for docking but as you go for QSAR studies Sybyl has many advantages over other softwares. Sybyl has the contour map feature which allows you to design new molecules......perhaps it is not found in any of the softwares till date.
Each tool u mention here, have their own remarkable things in there strategies in docking studies.. they jst vary in their flexibility of usage. publications with MOE wont change ur quality of work, go through citation in MOE website, u can find good journals there. In Glide nd Sybyl.. i goes with glide for docking studies, its matter of licence nd environment ur using(windows/linux).
All of your comments and questions are very interesting to me, as I am struggling with similar issues. The commercial products are quite expensive with rather large annual license fees. MOE and Sybyl have the advantage of being comprehensive packages that do not require modules or tokens, whereas Schrodinger and Accelrys require separate licenses or tokens for each component. For similar packages, I believe that the relative cost is Accelrys > Schrodinger > Sybyl > MOE.
My impression from reading articles and my own limited testing is that Accelrys is geared toward data management in the enterprise. Sybyl's particular strength is in cheminformatics and QSAR; they invented CoMFA and have an active patent on it. Schrodinger is especially known for its docking and scoring via Glide. MOE is interesting because of its potential for expansion and linking to other programs via its Scientific Vector Language (SVL). MOE also has a nice clean interface that unifies all the programs it uses. I like the fact that it can be used as a front-end for other software, such as NAMD for molecular dynamics and OpenEye Omega for generating conformers.
You might also want to look at Molsoft ICM Pro, which has a comprehensive package and good published results for docking. I am currently using YASARA-Structure, which is very reasonably priced, quite comprehensive, and extremely fair with respect to license policies. In my testing thus far, I have not found any product that is superior to YASARA with respect to accuracy of results, excellence of graphics, speed, customer support, or ease of use. I keep testing other products looking for the perfect all-around solution, but I keep coming back to YASARA. The only thing it seems to lack is the cheminformatics/QSAR components; it is geared toward protein structure and function, including docking and molecular dynamics.
In the end, however, the choice of software depends on what you will be doing with it. Moreover, the quality of results are highly dependent upon the care that is taken in preparing molecules and interpreting data. With this in mind, there is a wealth of free and open source software that is just as good if not better than the commercial packages, although the free software might not have as attractive an interface or be as easy to use.
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