Subject: Re: CCL:SYBYL

From: Renxiao Wang <[email-masked]>
Date: Sat, 5 May 2001 11:57:20 -0700 (PDT)

Dear Simon,

Good question. 

It is true that a lot of people are using InsightII, Cerius2, Quanta and
SYBYL in the area of computational chemistry/drug design. These softwares
usually provide a general interface, with which you can perform all the
basic modeling, and many add-in modules, which are developed for more
specific jobs, such as QSAR, docking, scoring, and so on.

I think all of these softwares are acceptable for the general interface. 
You many want to have at least one of them. As for drug design, my
personal choices are Sybyl and Cerius2. None of them is perfect though. 
For the specific "modules", the quality simply varies. Sometimes they are
far from reliable. You must be very careful when you use them since the
software company usually does not tell you that they may not work as well
as what you have expected.

There are a lot of academic programs in exsitence, which can out-perform
those commercial softwares on a certain aspect. You may want to use some
of them as enhancement or supplement in your work.  Actually when an
academic program becomes so successful, MSI or Tripos will probably
purchase it and, after proper wrapping, put it into their all-in-one
products. You can find a lot of such examples in the softwares I mentioned
above. 

As one of the academic programmers, I would like to add some more
comments: I will be glad to see that they (or we) work in an open,
collaborating manner to develop a molecular modeling system of maximal
common interests. Think about Linux and you know what I mean.

All my best wishes,

Renxiao Wang, Ph.D.
Georgetown University Medical Center 

On Fri, 4 May 2001, Simon Cross wrote:

> Hi, I would like to get an idea of the range of software that people use
> for computational chemistry/drug design - do lots of people use MSI
> software like InsightII or Tripos software like SYBYL or do most academics
> use freeware of some kind? Are there any reviews that detail
> advantages/disadvantages for these packages?
> 
> Thanks in advance,
> 
> -----------------------------------------
> 
> Simon Cross
> School of Chemistry
> University of Nottingham
> tel. 0115 9514193
> Email: [email-masked]
> 
>