Subject: Summary: Molecular Modeling - expert opinion needed

From: "Liew Fui fah" <[email-masked]>
Date: Fri, 31 Mar 2000 12:39:04 +0800

Greetings,

I received a lot of mails request me to post a summary to CCL, and here it is. Thanks
for those who response to my questions. However, the requests for summary are more
than the responses. The original question was:

--------------------------------
Dear CCLers,

 Nowadays, Internet has become a tool for scientists in order to perform their work
efficiently. Almost very one of us relies on the Internet to have discussion, looking
for information and communicating with others. Indeed, through Internet we are
effectively engaged with research, publications and information sharing that need
collaboration with geographically dispersed colleagues.

 With a thought of fully utilizing the strength of Internet, I foresee there is a
possibility to develop a web based molecular modeling station/portal, that would
allow chemists to carry out experiment work, share information and modeling results
with just a simple login to the server through an Internet browser. The molecular
modeling engine, computing facilities and the working space are provided by the
station.

 In order to carry out an analysis on this idea, I need expert opinion from fellow
CCLers as to inspect the need and how should such a web based molecular modeling
station perform. Please kindly give your opinions from a user or developer's
perspective with respect to the following aspects. (These are some basic guidelines
for the survey, you are most welcome to add additional comments)

 A. Interface
 - What are the interface features that you would like to see and use when
   manipulating your structure? Beside the common editing and browsing tools, you are
   welcome to suggest new feature the meet your requirements.
 - Would you like to have an interface setting that match the way you want to work?
 - How do you like the information of transition states, molecular properties,
   orbitals, vibration, electronic spectrum, etc to be displayed?
 - Which molecular modeling package(s) that has the user interface that you like most.

 B. Modeling Methods
 - What are the general features / methods that are a *must* for a molecular modeling
   package?
 - What modeling methods are you using?
 - What are the advance characteristics of a molecular modeling package that will
   meet you requirements?
 - Please suggest the molecular modeling package(s) that you like to use most in
   terms of it accuracy and ease to use.

 C. Platform
 - Since it will be a web based molecular modeling station, it is ideal to have
   access from multi-platform machine. As a reference, please suggest the platforms
   that most of the chemists engage with while they carry out their work.
 - Would you like to have a direct access to the web based station at your current
   working platform?
 - What platform do you think that is most capable to operate as a server which can
   handle large amount of job load and provide enough storage?

 D. Technologies
 - Do you think that Java will meet most of the web based application requirements
   while incorporating various plug-ins and formats (e.g. XML, SVG). What is your
   comment on this particular technology?
 - Please suggest other technologies that you think is powerful in developing a web
   based chemical application. (if any)

 E. Database
 - What are the existing databases that you would like to use in your searches?
   Please provide references.

 F. General
 - What do you think about a web based molecular modeling station/portal?
 - Will it be convenient to do molecular modeling job in a remote machine through
   Internet?

Your opinions and comments are very useful to my research, please kindly reply to
[email-masked]

Thanks.

Regards,

Liew Fui Fah,
University Malaya, Malaysia.
[email-masked]

Here comes the responses:

1)
Date: Wed, 15 Mar 2000 14:39:43 +0800
From: mcbskt <[email-masked]>
Reply-To: [email-masked]
Organization: Institute of Molecular & Cell Biology
To: Liew Fui fah <[email-masked]>
Subject: Re: CCL:Molecular Modeling - expert opinion needed

There are many on-going international collaborations in US and europe that will
address the questions.  Check the Pacific Symposium of Biocomputing.

========================

2)
Date: Wed, 15 Mar 2000 10:49:38 -0600
From: Kirby Vandivort <[email-masked]>
To: [email-masked]
Subject: [Fwd: CCL:Molecular Modeling - expert opinion needed]

What you are proposing sounds very similar to what we are working on right
now for Structural Biology.  I invite you to take a look at what we are
working on and offer any comments or suggestions.  We are relatively early
in the funding (about 1 year into a 4 year project) but we have an
initial release that you can play with.

http://www.ks.uiuc.edu/Research/collaboratory

If you have any questions, let us know!

Kirby

Kirby Vandivort                      Theoretical Biophysics Group
Email: [email-masked]          3051 Beckman Institute
http://www.ks.uiuc.edu/~kvandivo/    University of Illinois
Phone: (217) 244-5711                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA

3)
Date: Wed, 15 Mar 2000 15:03:37 -0600
Subject: FW: BioCoRE - a structural biology portal
From: Gila Budescu <[email-masked]>
To: <[email-masked]>

Please look at  http://www.ks.uiuc.edu/Research/collaboratory/
for an instant fulfillment of your wishes. The project started on 2/99 and
first official release was announced on 2/2000. We are looking forward to
supporting your work.
Gila Budescu

Barry Isralewitz     Theoretical Biophysics Group    Beckman 3121
Office Phone: (217) 244-1612     Home Phone: (217) 337-6364
email: [email-masked]     http://www.ks.uiuc.edu/~barryi