RDKit in Docker

Dcoker is an open platform for distributed applications for developers and sysadmins. I tried to use it. My PC is Mac Book Air, with OSX Marvericks. VirtualBox and Homebrew indtalled at first. Then I tried following steps. step1 From terminal, I installed docker and boot2docker. After that, docker and boot2docker command will use from terminal.Continue reading “RDKit in Docker”


After mishima.syk #4

Thank a lot for all attendance and presenters at mishima.syk #4 ! I enjoyed the event and party. All presentations were very interesting and exciting. ;-) I made brief introduction about cytoscape.js, and up loaded my slide and sample code to slide share and git hub. slide link code link My sample apps will needContinue reading “After mishima.syk #4”


 先週は某ソフトのユーザー会に参加してきました。 今回はバイオロジーよりの話題が多かったですが、 基調講演を始め非常に内容の濃い発表が多く大変有意義な時間を過ごすことができました。 個人的にはQSARを如何に、どこで活用するかの議論、前日のセッション、大変勉強になりました。 まだまだ自分には足らないことが多いと改めて実感して帰ってきまして今後に繋げていこうと思っている次第です。 スタッフ、役員、参加された皆様どうもありがとうございました。 来年は三島で、、、!?

Moleculer Similarity

Sometime, we discuss about molecular similarity. I think that meaning of similar is depend on a situation. For example, if aromatic pharmacophore is important, phenyl and pyridil maybe similar. But If molecular charge is important, phenyl ando pyridil maybe unsimilar. So, Having some metrics methodologies are useful. RDKit has interesting fingerprint called “Fraggle Fingerprint” It’sContinue reading “Moleculer Similarity”