Why We Hate Cilantro

I want to analysis SNP in coding region of olfactory receptor. In 2012, researchers studied SNP correlated with cilantro preference, and they found an SNP rs72921001 influence people’s feeling of cilantro. They said rs72921001 is a frequently accured SNP (an A -> C in DNA sequence) in OR6A2, an olfactory receptor.

Resonable, right? I immediately think this could cause an amino acid missense mutation. However, when I searched this SNP in Ensembl, I found it is located at upstream flanking region of OR10A2, and OR6A2 is another gene… Now I think maybe the name is changed during this time, and rs72921001 might influence the expression of OR10A2 in gene level… Umm.

Can I get more imformation of SNP in olfactory receptor? Let’s try by R!

Read more »

Protein contact map is a very helpfull tool to represent 3D protein structure in a 2D matrix format. More detail about contact map can be found here. Contact maps can not only be used as illustrations of protein, but also as tools to predict homology protein structure, especially for low homolog in evolution. Some scientists have already applied deep learning on this project and developed programs for structure prediction, such as RaptorX of TTIC.

There are several tools or program for calculate and display contact map on internet, here is an collection of them. I had a project several month ago, and I wanted to use a script to generate contact maps for a molecular dynamic trajectory, so that I use python to write a script to do it. I love python because I could always find usefull packages from internet. Here I found a package named MDtraj, And a package from Benjamin Rafferty (doi:10.4231/D35M62761)! Thanks to them, I can simply achieve my idea.

Read more »

Recently, I read blog from iwantobipen and found a python package for drug design, and it is called Open Drug Discovery Toolkit (oddt). Based on RDkit and OpenBable, it has two amazing function:

  • ligand-protein interaction finger print
  • electronic shape similarity calculation

Here I want to show you about the function of interaction calculation. All interaction, even including halogen bond, pi-pi stacting and cation-pi intercation.

Read more »
0%