Call rdkit from pymol

PyMol is one of major tool for visualisation of protein, ligand, etc. You know ‘Py’ means that pymol is written using python. I want to embed pymol to web app but it’s difficult for me (technical reason..) If anyone have advice to do it, please leave comment. ;-) Next, I have one question that, pymolContinue reading “Call rdkit from pymol”

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Make Docker image File with Chemoinformatics toolkits.

Docker https://www.docker.com is an open platform for distributed applications for developers and sysadmins. Providing docker image that means every one build same environment easily. It’s means create own image and share image. Docker provide container. Containers running on a single machine all share the same OS kernel. It’s difference of normal VM. I used dockerContinue reading “Make Docker image File with Chemoinformatics toolkits.”

New version of RDKit

Some days ago, new version of RDKit (2015.09.01) was released. I’m looking forward to this release. A lots of bug fix and new implementation was. I really thank to developers. Mac user can install rdkit using Homebrew ! (anaconda is not yet) I installed rdkit using homebrew, there are no trouble in El capitan. OneContinue reading “New version of RDKit”

Set up GPU for chainer in OSx El Capitan.

I enjoyed a UGM that held on Nov. 5, 6 and hope participants also enjoyed the meeting. One of the topics of the meeting was “Deep Learning”(???). I introduced about python library for deep learning called ‘chainer’ . I presented my challenge to build model for QSAR, using chainer but results were ….(Hahaha) Chainer isContinue reading “Set up GPU for chainer in OSx El Capitan.”

fish for drug discovery

Some years ago, I was interested in phenotypic screening that use zebrafish. In drug discovery project, we use animal models (often use rodent) to estimate efficacy, safety or etc. Also Knock out/in mouse is used for target validation. It’s still high cost and low throughput step. So, I think zebrafish is one of the interestingContinue reading “fish for drug discovery”