Message

Unfortunately, I have not worked with Sybyl = long enough=20 to really understand its advantages. On the other hand, I have used = InsightII=20 and AMBER much during the past 2 years. I agree with Fred that = Insight II=20 is powerful for homology modeling and that Sybyl is very good for small=20 moleules. The downside of Amber is of course that it uses command lines, = not an=20 interactive GUI. Still, I obtained very good models from Amber=20 and InsightII (protein models that is!) and acceptable models in = Sybyl=20 (small molecules). The problem with Sybly is that its conformational = searches=20 for macrocyclic molecules still remains to be improved. When I finished = my=20 studies and started my new job, my first objective was to choose a = modeling=20 software (for small molecules) for which we would be able to make = protein models=20 for rational design down the line. We were looking for a cost effective = software=20 that would not require buying expensive computers (I was setting up the=20 Molecular Modeling department for a new Biotech). Looking around, I came = about=20 MOE (Molecular Operating Environment) from the Chemical Computing Group = (CCG=20 Inc.) based in Montreal, QC. What is really interesting about MOE is = that there=20 is only one price for the entire package (it is not modular) and the = price is=20 VERY reasonable. Moreover, MOE runs on everything but MACS for the = moment!!!!!=20 So not only can you run it on a PC for cheap, you can also run it in = windows if=20 you cannot afford to hire a Linux administrator (check out http://www.= bio-itworld.com/archive/071102/linux.html for=20 a review about cost effectiveness of using Linux). There will obviously = be some=20 loss in computational power but it may be worth it = ...

Anyhow, MOE can perform everything from small = molecule=20 modeling to large proteins, docking, flexible alignments, etc. The only = thing=20 they are missing at the moment is a particular section to handle NMR = data. It is=20 very user friendly and can be very easy on the point and click side to = get what=20 you want (maybe just a littlle too easy sometimes!). I don't = understand why=20 MOE doesn't make it in these CCL archives because I know a several large = pharmas=20 that use it and love it, along with academic researches and = undergraduate=20 programs using it to teach molecular modeling techniques. With respect = to price,=20 performace, and flexibility of use, I (would like to) believe MOE will = start=20 taking a large segment of the industry. Moreoever, their supprt is = extensive and=20 rapid. Take a look at http://www.chemcomp.com for = more=20 details. The only disadvantage of MOE is that they haven't been around = for a=20 very long time and sometimes lack the vision of a molecular modeler, but = they=20 are keen to learn. MOE was developped by programmers, not molecular = modelers so=20 you can modify the entire MOE environment with a bit of programming=20 skills. Moreover, I find interesting tools that were developed by = CCG for=20 model analyses (tools that I did not have the chance to discover in = other=20 programs if they exist). Needless to say, I'm convinced that MOE is a = serious=20 competitor to the other more traditional programs. On the other hand, = I'll say=20 the same thinig to you as a molecular modelre at Pharmacia told me: "... = not one=20 program can perform everything you need which is why you need them all = ;o)" .=20 MOE on the other hand, comes close to completeness in my opinion ... I = haven't=20 had to get other programs yet (I've had it for 9 = months).

for quite a while now, I am pondering about the folling: why is it = that=20 most of the modellers use Sybyl rather than InsightII? In most = publications,=20 people say in the methods section (or elsewhere) that they used Sybyl. I = was=20 told once that InsightII was more powerful, once you get to know it, but = since I=20 have never used Sybyl, I cannot really compare.