Blog 2

These past few weeks, I have been working on familiarizing myself with molecular dynamics and understanding how big of a role they play with our research. Molecular dynamics is a computer based stimulation which helps analyze atoms and molecules that are moving and in which ways they interact with one another. This technique helps us work with protein models and experiment different methods of combining them. Protein modeling is a very effective way that helps obtain structural information before researchers start experimenting in labs. With the help of “Amber Tutorials” we can see the motion of protein models and be able to design different sets of proteins that are arranged in various ways with computer coding. MD stimulations aids in finding a more accurate model of the target protein and predict any changes in the function of the protein.

Dr.Deng has been very busy this semester so I have been working on reading up on how to use Amber and master all of its tutorials. I have ran into problems several times where the program either stops working or does not allow me to insert a certain set of codes therefore I ask Professor Deng for assistance and he is usually able to help me. Amber is not a very effective program but it is great for beginners to use and familiarize themselves with the coding language. Later on, we will start using better programs that aid us in protein stimulations.






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