Molview Download

[Ceumar Pee]

Istarted doing some web development myself around that time and I decided thatI could make an even better, more visually appealing program. It took me quitesome time to find out how 2D structures could be resolved into 3D structures.The secret turned out to be the Chemical Identifier Resolver which can turn 2Dcoordinates into 3D coordinates. Unfortunately this service goes down for acouple of days from time to time which is still causing malfunctions in MolView2.4. For this reason, the Chemical Identifier Resolver will be replaced with aprogram running on the MolView servers in MolView 3.

I made MolView available on molview.tk (a domain which was still free backthen), showed it to a couple of people and considered the project to befinished. About a half year later I learned about Bootstrap, a user interfaceframework for websites built by Twitter. It looked quite stylish so I rewrotethe user interface of MolView using this toolkit.

Because of the redesign, MolView had gained my attention once again and Iimplemented a search tool for PubChem (small molecules) and RCSB (proteins).In the mean time the design got more complicated and Bootstrap was not reallysuitable anymore so I developed a new, handwritten design to seamlessly fit allfeatures in one interface (for some reason black became the primary color).

The 1st of July 2014 is the day that molview.org was launched. This new domaincontained the first version of the 2.x series. One of the most exciting newfeatures in this version is the integration of the Crystallography OpenDatabase enabling users to view crystal structures. I also discovered git andversion control (keeping track of your code) around this time. MolView 2.1(basically the same as v2.0) is the first version which is safely stored onGitHub.

I improved MolView a lot during the summer of 2014. MolView got a much whiterdesign and an autocomplete feature to quickly find proteins, small molecules andcrystal structures. This is particularly useful for the crystal structuresbecause the Crystallography Open Database does not have a search index(therefore searching it is relatively slow). The protein collection which youcan find via the autocomplete is derived from the Molecular Machinery Posterfrom the Protein DataBank.

Draw your 2D molecule and then visualise it as 3D using MolView. This platform is FREE and you can use it straight from your internet browser. The 13-minute video tutorial shows how you can draw your chemical compound(s) in MolView and then convert it to 3D. This platform would be useful for students and researchers since it can be learned quickly and lets you visualise molecular structures easily. Plus, you can do quick search for drug information from PubChem in MolView. This resource and platform would also benefit instructors who are conducting online teaching and learning activities, and for students doing self-study #molview #3D #visualisation

MolView is a web application which helps students and teachers to visualize molecular structures and view their properties. There are numerous databases publicly available to provide the required data such as PubChem, ChemSpider, ChEMBL, DrugBank, the Crystallography Open Database[1], and many more.[2][3] Currently, MolView uses PubChem, RCSB, the Crystallography Open Database, the Chemical Identifier Resolver[4], and the NIST WebBook[5] to retrieve data. MolView offers a simple search interface to find small molecules, proteins and crystal structures in these databases. MolView uses JavaScript libraries, that use modern web technologies such as WebGL, to visualize these structures. In the past year I have designed a new version of this application from the ground up to facilitate the implementation of new databases and tools. Along with a new architecture and user interface, this version will include internationalization, interactive instructions, advanced search tools, more import/export tools, and more presentation tools. I also intend to include more computational chemistry tools to make the analysis and processing of complex data easier and more fun.

In recent years web technologies have come a long way. The usage of browser plugins, such as Adobe Flash and Java, for the development of advanced applications in websites, has been replaced by built-in JavaScript APIs such as WebGL[6] and Web Workers[7]. The market of cloud computing(a) has skyrocketed, partially due to the vast increase of big data(b).[8][9] New standards for database APIs(c), such as REST and JSON(d), have emerged and are now used by almost all public API's on the internet including some major chemical databases like PubChem, ChEMBL and PDBe. I think these developments have opened many new opportunities in cheminformatics and bioinformatics.

MolView started out as 2D to 3D structure converter where the user can draw a structural formula and view a generated 3D conformer that was generated using the Chemical Identifier Resolver(e). The ability to search by name using the Chemical Identifier Resolver was added later as an experimental feature. This turned out so well I added integrations for PubChem, RCSB and the Crystallography Open Database. Now MolView has become an example of what happens when you bring modern web browser technologies and online scientific data resources together. MolView is available free of charge on molview.org since 1 July 2014. The user base is still rather small (>10k sessions per month) but is growing rapidly.

You might be wondering what you can use MolView for today. The best way to find out is, of course, to visit molview.org and try it out for yourself. To get you started, here is a list of things you might want to try. Each section is also demonstrated in a YouTube video.

You can draw organic molecules in the sketcher on the left side. By default the sketcher shows the structural formula of caffeine. Clear the sketcher by clicking the trash icon in the top-left corner. Then draw a new structure using the sketch tools. You can for example draw a benzene ring, an individual atom or a bond. When you are done drawing the structure, convert the structure to 3D using the '2D to 3D' button in the top-right corner of the sketcher. You can now view and interact with the 3D structure.

You can also search for chemical structures. Type a molecule name into the search input in the top-left corner of the window. The search input will display a list of suggestions from PubChem, the Crystallography Open Database and RCSB. When you have loaded a structure, you can enable a measurement tool via the Jmol menu. MolView uses the JavaScript variant of Jmol (JSmol) for the measurement tools.[10] When you have enabled a measurement tool, you can click atoms in the viewing window to measure distances, angles and torsion angles.

Jmol has many powerful computational tools and a few are currently directly accessible in MolView. You can for example render a Molecular Electrostatic Potential surface of the loaded 3D molecule. If you connect a fluorine atom to a hydrogen atom and render a translucent MEP surface, you can clearly see that the fluorine atom attracts electrons much stronger than the hydrogen atom. You can also run an energy minimization via the Jmol menu. This can be useful when the loaded structure is resolved using the Chemical Identifier Resolver. The Chemical Identifier Resolver uses CORINA, a program that splits the molecule into ensembles, looks these ensembles up in a database and assembles them back together.[11]

You can load small crystal structures from the Crystallography Open Database via the search interface. The blue suggestions from the search input are mineral names from the Crystallography Open Database. Additionally you can search trough the entire Crystallography Open Database via the search menu. After you have loaded a crystal structure, you can render a supercell model via the Model menu.

Just like small molecules and crystal structures, macromolecule's can also be loaded into MolView. MolView can retrieve biological macromolecule's from RCSB. You can switch between different color schemes and protein structure representations via the Protein menu.

You can also view certain spectra. To do this, you first have to load or draw a molecule. Then you can open the spectrum viewer via the Tools* menu where you can choose from different spectra. IR and mass spectra are fetched from the NIST Chemistry WebBook. A H1-NMR prediction is calculated using *nmrdb.org.[12] When you select a spectrum, it will be loaded into the interactive spectrum viewer where you can read out the values.

If you write web articles that involve chemistry, the embedding tool from MolView might be just what you need. You can get an embed code for every 3D structure in the viewer by opening the embedding dialog via the Tools menu. You can then paste this embed HTML code into your web page. In future versions you will be able to embed more content such as the spectrum viewer and the sketcher. Below is an example of an embedded caffeine molecule.

Over the past years numerous ideas for new features have come up. I'm now writing a new version with a much higher level of modularity than the current one. This will help me to integrate new exiting stuff. Apart from quite a number of new database integrations, I want to focus on the three other subjects: visualization tools, sketch tools and tools for teachers. The next three sections will explain these subjects in more detail.

Currently MolView uses GLmol, JSmol and ChemDoodle Web for 3D visualization.[13][14] In the last few years more mature web viewers for molecules have been developed that will replace the current viewers (except for JSmol of course). These viewers include 3Dmol.js (organic molecules, fork of GLmol), PV (simple viewer for proteins) and NGL (advanced viewer for proteins).[15][16][17] But viewing 3D models is not the only visualization tool I intend to offer. An interactive NMR viewer like the one on nmrdb.org might finds its way into MolView pretty soon. And perhaps even a DNA sequence viewer/explorer.

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