Subject: Molecular Modeling - expert opinion needed

From: "Liew Fui fah" <[email-masked]>
Date: Wed, 15 Mar 2000 11:28:44 +0800

Dear CCLers,

Nowadays, Internet has become a tool for scientists in order to perform their work efficiently. Almost every 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]