Molecular Dynamics

This is a big big subject and I am no expert in any of the aspects involved.  My summary is that it allows me to compute how one molecule interacts with another one.  My primary objective is to find those drugs which will best alleviate the damaging aspects of myeloma and any other complaint. My interest has spread to considering which bacteria are active in the gut and how which drugs effect them and similarly which molecular structures  are present in toenail fungus and how they might be subdued.

I hope to demonstrate by example how 2 or 3 drugs can interact with 2 or 3 proteins.  None of this is validated, it is possibly riddled with errors; but it has given me a basic understanding of how to go about the topic.

Firstly this is a computing activity; you need a computer.  Many of the calculations are long and complex so if you intend to look at the topic seriously then you need a good computer.  I am familiar with Windows so I use that , but quite possibly Linux would be a better choice.

You also need software and usually need to download the package applicable to your hardware.  If you intend to get into serious computation then get a good computer first and all software can be selected for that machine.  In particular one of the software packages called NAMD has been written to utilise CUDA processing,  so a multi-core CPU with multiple graphics cards using multiple CUDA cores will speed up your computation by a very large factor.

I have gone for a 6 core Intel 64 bit with dual CUDA nVidia 900 series graphics cards and solid state disks;  running Windows 8.1.

The software I use is:


It can all be found on the web.

What is an aminoacid?  It is a chemical, there are 22 different ones in humans, each given a name, a 3 digit code and a short 1 letter code.  They make up everything we are.  There is one called alanine (given the codes  Ala and A) comprised of 3 carbon , 7 hydrogen , 1 nitrogen and 2 oxygen atoms. Another of the 22 is called glycine (G).  The critical issue is that they can all be joined together in a string of animoacids.  I call this a "stam".

Descriptions of proteins etc ( and the DNA that defines their construction) are abundant on the web.  I only intend to describe one or two examples.  I will use the word stam to mean any string of aminoacids whether they should more properly be called proteins , kinases , peptides , or enzymes.

My first example will be a look at toenail fungus  and the second is an example in myeloma.  Both of these make reference to drug selection


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