Talk:Molecular modelling

Merging molecular models and moleculer modelling?

I believe that molecular models (sic) are different from molecular modelling. In that article I suggest the emphasis is on physical models like Nicholson, Dreiding, Wooster, Beevers and many other classics of physical construction. Some of these existed well before the development of computers. The disticntion is similar to that between computer puzzles and puzzles using physical objects - there is sufficient interest in each. I will outline this on the page Petermr 17:24, 9 May 2006 (UTC)

I have now completed the first draft of the article and I hope this shows that this is a significantly different topic from the one here. I expect that more examples of physical models and more photographs will be added, especially to capture the history.Petermr 21:39, 9 May 2006 (UTC)

I completely agree with Peter that those things are completely different. I can not see any reason for a merge.

And, Peter since you are the expert knowing those things you should add also some references about the mentioned terms. This will allow non-experts to contribute having a look at those references, e.g. students. Nobody starts as expert ;-) JKW 22:59, 9 May 2006 (UTC)

Merge request was removed. JKW 19:33, 14 May 2006 (UTC)

Spelling

Most authors use the term Molecular modeling rather than modelling. Please change lemma and redirect. 131.220.136.195 11:50, 27 September 2006 (UTC)

Most? Err... sure... (American and British English spelling differences#Common suffixes). --Van helsing 18:22, 26 October 2006 (UTC)

Search Google and Amazon for both typings and you will see... 80.136.236.202 11:39, 25 November 2006 (UTC)

Molecular modeling is not only MM and MD

I think molecular modeling is much wider than MM and MD. First, it can be aimed at solution of many different problems, including enzymatic catalysis, packing of molecules in crystals, behaviour of fluids and solid state, ligand docking, protein structure prediction, homology modeling, etc. It can also utilize different methods, including "manual" manipulations (using bond rotations and movement utilites incorporated in different molecular graphics programs, such as Quanta), Quantum Chemistry calculations, energy minimization with different MM force fields, MD, distance geometry, software for building regular structures or crystals or optimaization of spatial positions of proteins in membranes, etc. I think MM and MD should not be described here, but just referred to the corresponding MM and MD articles that already exist. What do you think? Biophys 15:25, 28 October 2006 (UTC)

More terms are available under computational chemistry and according to the book "A. Leach, Molecular Modelling, 2001" it is indeed a broader term. In fact the following terms contain a lot of redundancy and it is unclear how we should suggest a good merge request?

* force field (chemistry)

* molecular mechanics

* computational chemistry

** and if we use the definition there

uses the results of theoretical chemistry incorporated into efficient computer programs to calculate the structures and properties of molecules and solids,

then cheminformatics and computational chemistry are interchangeable. What is the key difference? The focus of computational chemistry on energy based methods and the focus of cheminformatics on combinatorial problems (Combinatorics, Combinatorial chemistry, library design , docking). And both interchange those principles, since docking is also part of computational chemistry. Has anyone a good reference to answer this question?

JKW 16:49, 28 October 2006 (UTC)

One good place to look is Encyclopedia of Computational Chemistry (5 volumes) [[1]]. I saw it in the library of our University. It is very solid and well written. We should check how everything is organized there. Biophys 23:52, 29 October 2006 (UTC)

It is indeed well written in general, but it is not too well organised. I think in many cases they picked authors and they wrote what they wanted to. For example there is an article on spin coupled valence bond, but nothing specific about other modern valence bond methods, as the article by Shaik is too specific. It is however worth checking to get some kind of reality check on our articles in comp chem. --Bduke 00:09, 30 October 2006 (UTC)

I looked through some of those articles in Encyclopedia of Computational Chemistry. You are right. For example, it is completely unclear why someone decided to develop OPLS or CFF. Are they better than AMBER? If they are better, then what exactly is better? I have no idea. Biophys 15:10, 5 November 2006 (UTC)

No, I think all articles, such as force field (chemistry), chemoinformatics, molecular mechanics, etc. must stay separately, as they are right now (they describe related but different subjects). However, this article about molecular modeling should mostly refer to all these more narrowly defined articles (such as chemoinformatics, molecular mechanics, etc.) and do not repeat their content. Biophys 18:08, 7 November 2006 (UTC)

The above written statement are correct to best of my knowledge. Thanks

This discussion is old, but should be discussed again. The previous comments are completely correct. Molecular modeling can refer to the large number of techniques used to model molecules: molecular mechanics, electronic structure (including density functional theory, etc.), plus others. Molecular modeling does not refer to just MM or MD. Practitioners in the field often use the terms molecular modeling and computational chemistry interchangeably. I think the topic should be changed to a more generic description with links to separate topics. The current article seems to imply that molecular modeling only refers to molecular mechanics methods. Just google for books with 'molecular modeling' in the title and you'll see lots of books covering a wide variety of topics, not just molecular mechanics. Che kid (talk) 16:24, 3 January 2012 (UTC)

Modeling is an applied science

One aspect that needs to be emphasized is that molecular modeling is applied science. As mentioned earlier this can included automated applications of theory or more manual GUI-driven manipulation of molecular systems. The article should focus on the various aspects of molecular modeling and the applications and then direct to more detailed versions of those topics as has been mentioned earlier

dsingh 19:32, 24 May 2007 (UTC)

Lost MCBs

Several MolBiology pages link hereas they should link to Mathematical biology --Squidonius (talk) 18:52, 20 November 2007 (UTC)

Move to different spelling

I think it is unfortunate that this article has been moved from "Molecular Modelling" to "Molecular Modeling" without discussion here to get consensus. The category for which this is the main article still has "ll". I have edited the category here and in one other place to point to that actual category. However if is this move is to be retained, the category needs to be moved also and all references to the category altered. Note too that Leach's book should still be "Molecular Modelling" because that is how it is titled, as it was published in the UK. --Bduke (Discussion) 22:00, 19 November 2008 (UTC)

I've reverted the move. Per WP:ENGVAR, the "dialect" in which the article was started should be retained. --Itub (talk) 11:19, 21 November 2008 (UTC)

InsightII and Ceruis2

I work for the company that makes these products (no names right now). I would like just to change the links so they work but don't want it to be "advertising" as such-- though I see other companies' products are listed. Do you think that would be acceptable? SimonTrew (talk) 04:26, 5 March 2009 (UTC)

Links

I propose to leave the red links, as an invitation to write articles, but be sure to maintain the external links upto the writing relevant articles. For example, as I did with a broken link MOE. P99am (talk) 08:25, 7 April 2009 (UTC)

But it was not a red link. It was (and is) a link to a disambiguation page. SimonTrew (talk) 10:11, 7 April 2009 (UTC)