blog of personal interest
I enjoyed 18th mishima.syk meeting at last weekend. I think the community is really cool and worth to join for caching the cutting edge of chemo/bio informatics ;) Feel free to participate and present here if you have interest the meeting. In the meeting, yamasakit_ introduced “Rust basics” with live coding! Fortunately his presantation materialContinue reading “Use RDKit from Rust v2 #RDKit #Rust”
Kinase is one of the attractive target for drug discovery. So there are lots of data not only protein but also inhibitor available. ChEMBL is useful public data source for Kinase inhibitor data however to use the data, we need to retrieve data from the DB and curate it. Of course there are commercial databaseContinue reading “Make curated Kinase inhibitor dataset from ChEMBL30 #memo #chemoinformatcs”
Recently, ChEMBL ver. 30 is released. I’ve installed it in my PC and added rdkit schema ;) And current chembl ftp site provides monomer library of HELM. @magattaca posted really useful blog post in Japanese https://magattaca.hatenablog.com/entry/2020/11/25/004829. The post describes about HELM, its monomer and render these monomers. I’m interested in how to build peptide fromContinue reading “Build peptide from monomer library from ChEMBL #RDKit #ChEMBL #Chemoinformatics”
Recently I posted really useful package named molplotly. The package can make interactive plot with compound structure as hover. Inspired the activity, I tried to wrote code for making chemical space mapping with interactive rendering of molecules. Base code came from my previous post. There small changes in dash part because of I used newContinue reading “Make interactive chemical space plot with Dash #RDKit #useful_rdkit_utils #Dash #Chemoinfomratics”
Some days ago, @WillMcCorki1 introduced really cool package named molplotly. Thanks for sharing the information. Molplotly is add-on to ploty for rendering molecular image on mouseover like TIBCO Spotfire. The package(https://github.com/wjm41/molplotly) uses JupyterDash for integrating JupyterNotebook so it’s easy to embed interactive chemoinformatics chart in JupyterNotebook. However, it’s difficult to use the package from outsideContinue reading “Integration of molplotly and Flask for developing chemoinformatics web app #RDKit #molplotly #Flask”
SMARTS which is a language for describing molecular patterns like regular expression for NLP is really useful for chemoinformatician. However it’s difficult to understand due to difficulty of visualization SMARTS query. As far as I know, there are few software which can visualize beautiful SMARTS pattern. BioSolveIT provides unique SMARTS editor but it’s required commercialContinue reading “Easy way to visualize SMARTS #chemoinformatics #memo”
Matched molecular pairs are popular approach to transform molecules with prior knowledge of medicinal chemistry. MMPDB is useful open source package for managing MMP dataset which is derived from GSK under the 3-clause BSD license. It is easy to use and work really fast. I love it the package. However current version of MMPDB supportsContinue reading “Let’s update MMPDB #RDKit #mmpdb #Chemoinformatcs”
I love flask and django for making web app and often use Flask for web app development. Sometime the app will serve files after getting user request. In this case, static files which are generated by the app will be stored in static folder. And the folder will store lots of files. So I wouldContinue reading “Define a function after the request #Flask #memo #python”
Recently Rust is becoming popular language and I have interest Rust. There is a hurdle for me to move programming language from python to others because I would like to use RDKit from my coding environment for chemoinformatics tasks ;) As many chemoinformaticians know that recently rdkit provides new C Foreign Function Interface (CFFI). AndContinue reading “Use RDKit from Rust #RDKit #rdkitcffi #Rust”
I believe that all chemoinformatian think RDKit is really useful package for OSS chemoinformatics tools ;-) RDKit provides lots of useful function not only to build 2D based predictive model but also to make 3D structure from 1D/2D molecules. However sometime we need to write code of routine task, for example molecule to bit vectorContinue reading “Let’s use RDKit more conveniently! #RDKit #chemoinformatics #useful_rdkit_utils”
Some days ago, I made a post about openmm_runner. Previous code can’t calculate MD which contains metal ion such as Mg2+. I wonder that does openmm can handle metal ion. I asked the question in the openmm community and could get the answer ;) I know that ‘Amber14 includes parameters for Mg2+ as well asContinue reading “Update of openmm_runner #moleculardynamics #TeachOpenCADD #rdkit #openmm #chemoinformatics”
As chemoinformatitians know that TeachOpenCADD(TOCADD) is one of the really useful site for learning in-silico drug discovery pipeline. It supports wide range of chemoinformatics not only LBDD but also SBDD. New version of TOCADD supports Molecular dynamics(MD) tutorial with openmm. The talktorial T019 and T020 show how to run and analyse MD with openmm andContinue reading “Make mdtools for openmm #moleculardynamics #TeachOpenCADD #rdkit #openmm #chemoinformatics”
I’m writing the post on the Shinkansen. Counting from 2020, we’re still in the COVID-19 pandemic. My life style is dramatically changed before / after the pandemic. But still continuing the blog ;) Here is the access log of the site. There are more unique visitors (deep blue bars) in 2021 compared to the lastContinue reading “Look Back at 2021 #diary”
Long time ago, I wrote post about the same topic. The code used old version of rdkitjs and electron. Recently rdkitjs is maintained in official repository so I would like to re-test the approach. My old post is here. To do the following approach, I installed node.js, electron and npm at first. Then init theContinue reading “Create desktop chemoinformatics application with JS #chemoinformatics #RDKit #JS”
I wrote a Japanese post about PAM/NAM about mGlu family yesterday. As I mentioned that, small difference of molecules makes big difference of these conformations. I tried to check it with ETKDGv2 method which is implemented in RDKit. The approach is based on Molecular Mechanics(MM) so I would like to check it not only butContinue reading “Compare torsion drive results between C and O linker of specific structure #qcportal #souyakuAC2021”
最近何故か複数のサイトを管理しているiwatobipenです。ちなみにこのサイトのBlog更新頻度が低下しているのはそのせいではなく、純粋に忙しいためです。今年も残り後少し、早いものですね。 そして今年もまたAdventCarenderの季節になりました。 私はOSSやOpen Accessのジャーナルが好きです。もちろん職場でも自宅でも利用できるということもありますがそれ以上に良いコミュニティーが形成されているものが残るからです。さて、今日はACS系のジャーナルでOpen Accessのもので最近気になったものを紹介させてもらおうと思います。ACS Bio & Med Chem Au というジャーナルでACS系においては珍しくアクセスフリーです。カバー範囲もライフサイエンス系です https://pubs.acs.org/doi/10.1021/acsbiomedchemau.1c00033This includes experimental and theoretical studies on the chemical, physical, mechanistic, and/or structural basis of biological or cell function across all domains of life. で今回読んだのは以下の論文です。 Title ’Discovery of “Molecular Switches” within a Series of mGlu5 Allosteric Ligands Driven by a “Magic Methyl” Effect Affording Both PAMs andContinue reading “ACSのOpen accessのジャーナルから2021冬 #souyakuAC2021 #Japanese-post”
There are lots of way to define molecular similarity, for example fingerprint based, descriptor based, graph based, shape based etc. etc… In the 2D world, circular fingerprint based similarity is used in many case. However, 3D based similarity approach is also useful for drug design. As you now, OpenEye provides useful software named ‘ROCS’. ROCSContinue reading “Compare shape and electrostatic similarity of molecules #RDKit #espsim #python”
Recently there are lots of publications and codes for feature extraction with GCN of molecules. But fingerprint based approach is still useful due to GCN approach isn’t perfect. I often use the circular fingerprint such as ECFP / MorganFP for machine learning, clustering or other chemoinformatics tasks. Fingerprint based approach is still important I thinkContinue reading “Calculate Atom-Atom-Path Fingerprint with RDKit #Chemoinformatics #RDKit”
Recently there are lots of publications and patents about PROTACs (Proteolysis targeting chimeric). As name indicates that the target of PROTACs is the specific protein of degradation (POI) so it’s called chemical knockdown. Compared to inhibitor, sometime PROTACs shows a strong biological activity. It’s an interesting approach. And I found another interesting approach in ACSContinue reading “A memo about New approach of Drug discovery from ACS medchem letters #memo #journal #RIBOTAC”
Molecular dynamics (MD) simulation is one of the useful approach for estimating protein-ligand interaction. However, computational cost of MD simulation is high, so large computational resource is required when we run the large scale MD simulation. On the other hand, now we can use freely available could computational resource such as Google colab. It’s notContinue reading “Run MD simulation with cloud resource #openmm #google_colab”
Is life worth living? 