Subject: Modelling software

From: Simon Cross <[email-masked]>
Date: Tue, 15 May 2001 17:42:19 +0100 (BST)

Hi all, some time ago I asked which software tools people liked to use and
got a range of responses. I have compiled the replies below:

-----------------------------------------

Simon Cross
School of Chemistry
University of Nottingham
tel. 0115 9514193
Email: [email-masked]

Date: Fri, 04 May 2001 17:06:10 +0100 From: Mark Forster
<[email-masked]> To: Simon Cross <[email-masked]> Subject:
Re: CCL:SYBYL 

Dear Simon 

We use a mixture 

(a) academic codes such as AMBER, Autodock etc, GAMESS. 
(b) Web based resources for sequence database searching, tools such as
    SwissModel for homology modelling. 
(c) Commercial tools such as insightII/Discover, Gaussian 98W. and choose
    the easist to use tool for the job. For interactive 3D model editing
    and other tasks the insightII tools are very comprehensive - hence it
    is hard to do without this completely. 

Mark

Date: Fri, 4 May 2001 19:24:42 +0200 (CEST) From: Bernd Rupp
<[email-masked]> To: Simon Cross <[email-masked]>
Subject: Re: CCL:SYBYL 

Hi Simon, the usage of InsightII or Tripos depens from the problem you. I
have no favoured packages. At this time i work at proteins so i work with
insight. Other time, when i work with small molekules I prefer sybyl. here
are some usefull sites whit a list of the most used programms: 

http://chpc06.ch.unito.it/chem_linux.html
http://sal.kachinatech.com/index.shtml Tshoe Bernd -- Bernd Rupp

Heinrich-Heine-Universitaet Duesseldorf | Gebaeude 26.23 Raum O2.33
Institut fuer Pharmazeutische Chemie | Tel.: 0211 / 81 - 1 38 27
Universitaetsstr. 1 | Fax.: 0211 / 81 - 1 38 47 40225 Duesseldorf |
E-Mail: [email-masked]

Date: Fri, 04 May 2001 13:38:18 -0500 From: Abby Parrill
<[email-masked]> To: Simon Cross <[email-masked]> Subject:
Re: CCL:SYBYL 

Hi Simon,
  
My group uses the following: MOE (Chemical Computing Group) Cerius2
(MSI) Amber6.0 (UCSF) Macromodel Gamess Dock/MidasPlus Autodock NACCESS
MM3 SCORE

> 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?

We are using Macromodel from Schrodinger (www.schrodinger.com).  For
academic pricing, our experience is that Macromodel is a good bit cheaper
than Insight (as stated on Schrodinger's web site, you can get a permanent
network license for a 255-address subnet for Macromodel for $3k, and I
seriously doubt MSI will discount the relevant modules of Insight down to
anywhere near that level). 

> From a computational perspective, Macromodel
is powerful.  Its weakness is that it is not so good for visualization.  
For visualization, matters of cost aside, I much prefer Insight.  I have
not used SYBYL or dealt with Tripos. 

Another package that you might want to look at is ICM from Molsoft
(www.molsoft.com).  It runs on a ton of different platforms, and offers
good visualization.  However, in some respects it is not as
computationally flexible as Macromodel (you are
limited to MMFF, and one company rep I talked to couldn't tell me whether
I could easily customize the force field).  I don't think I've seen their
pricing for the advanced modules of their program. 

-- Eric Bennett ([email-masked] ; http://www.pobox.com/~ericb )

Overall description: 

packages, like SYBYL and Insight II have one great
advantage : they have nice, more or less user friendly interface, so it is
easier to start working with them. However, almost all the subprograms,
included in those packages are available to academic users for free or
really small fee, so there is the freeware solution: Modeller - homology
modelling(free to academic institutions) Tinker - energy minimizations and
dynamics freeware FT-dock, Autodock, Dock - docking programs (free to
academic institutions) LigBuilder - Drug Design (free to academic
institutions). And, of course, plenty of visualization programs. The
disadvantage - command line and problems with the format conversions. So,
the choice is on you 

Yours Sincerely RNDr. Bruno Sopko Dept. of Biochemistry, Charles
University - Faculty of Science Albertov 2030 128 40
Praha 2, Czech Republic Phone: +420-2-21952173 Fax.:  +420-2-21952331

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 

Dear Simon, take a look at www.chemcomp.com 

The Chemical Computing Group has developed a "next generation" modeling
package. Besides covering the
application areas High Throuput Discovery (with more than 300 QSAR
descriptors built into MOE), focused library design, Homology Modeling and
Structure based Design, it has the major advantages of being platform
independent and coming with the source code. CCG has developed it's own
programming language (SVL), that allows for a 10 to 1 reduction in lines
of code. That makes it an ideal tool for both rapid software development
and teaching. CCG gives MOE for free, if you use it for teaching! Please
don't hesitate to contact me in case you have any further questions.

Sincerely, 

Dr. Wolfram Altenhofen Director of Scientific Services Chemical
Computing Group AG Wiesentalstr. 74a 79539 Lrrach Germany

From: Malcolm Gillies <[email-masked]> 

My take on Sybyl vs Insight (based on not all too extensive use of
either) is as follows: Insight has
the edge in forcefields (though you have to pay extra for many of them);
Insight seems better put together from a programmer's perspective, but
less intuitive in terms of basic editing of chemical structures; Insight
has more annoying bugs and quirks; Sybyl has more flexible tools for
manipulating proteins and DNA; Insight has a more substantial MD code
(Discover); Insight has better facilities for making publication quality
ribbon diagrams etc; the Insight user interface is easier for beginners.
Probably more important than any of these factors is the availability of
special-purpose modules, and file-format compatibility with external
programs. If you need to use FlexX, CHARMm, DelPhi etc, then your life
will be much easier if you choose the program with the best compatibility.
In the end, I used Insight more, and liked it less... cheers, 

Malcolm --

Malcolm Gillies <[email-masked]> Post-doctoral researcher
Organic Chemistry, Dept of Chemistry, Technical University of Denmark

From: Stephen Doughty <[email-masked]> To:
[email-masked] Subject: Re: CCL:SYBYL 

Simon, Across in Phamaceutical Sciences we use a wealth of different
software. Generally
MSI and Tripos are the molecular modellers tools of choice. Each has its
pros and cons, choices are usually made by what individual researchers cut
their teeth on. 

Personally I think Sybyl is the best modelling software (I
have that here), although it lacks some of the simple functionality of
some MSI products (I prefered Quanta, but it is now pretty much
unsupported; we have InsightII here at the moment). However, it more than
makes up for it in terms of advanced functionality. However, the
functionality you might want costs money. 

Free software - there's some good stuff out there now, VMD, WhatIf, NAMD,
plus a few others. Again, it
depends what you want to do - these are OK for modelling protein
structures, but some are better at building than others (some don't
include any building functionality at all). If you just want small
molecule modelling, look at Spartan or Cache. If you want to do any proper
modelling then you'll also need some molecular mechanics code - don't rely
on the force fields given in the programs, for proteins you'll want either
CHARMM or AMBER. 

Again, its horses of courses ... people (generaly) choose
the software based on the type of modelling that they are likely to be
doing. 

Let me know if you want more info or a more detailed discussion.
Cheers, Stephen