Assessing the innovation of new drugs #memo #journal #ACS

Measuring innovation is challenging task for many kinds of industry. To get IP, the invention is required not only inventive step but also novelty. So in the pharmaceutical industry it is difficult to assess compound innovativeness. Some days ago I read an interesting article which discuss this point and would like to share it. TheContinue reading “Assessing the innovation of new drugs #memo #journal #ACS”

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Install chemical cartridge for SQLite3 #rdkit #sqlite3 #chemicalite

I often use postgresql chemical cartridge of rdkit. It’s really useful for making structureDBs with opensource tools. I installed rdkit2020.0901 recently so I’m waiting to release of rdkit-postgresql for 20200901. ;) And also I often use sqlite3 for making localdb for convenience. However, sqlite3 can’t use chemoinformatics query such as similarity and substructure search. SoContinue reading “Install chemical cartridge for SQLite3 #rdkit #sqlite3 #chemicalite”

Store rdkit mol object into KVS #rdkit #tkrzw #chemoinformatics

As you know key value store is useful tool, it like python dictionary. Basically KVS structure is simple, it is constructed from key-value pairs. So it seems useful for storing compound_id and molecule pairs too. I used kyotocabinet before, however recently I found the successor named tkrzw. It was written by C++ but the developerContinue reading “Store rdkit mol object into KVS #rdkit #tkrzw #chemoinformatics”

Create macrocyclic mol object from sequence #RDKit #Memo

Good morning ;) I knew interesting method ‘MolFromSequence’ in RDKit UGM2020. It can build molecule object from amino acid sequences. It means that I can get mol object from amino acid sequence such as ‘GGGG’ ;). And recently, macro molecule is the one of interesting strategy for drug discovery. So I would like to testContinue reading “Create macrocyclic mol object from sequence #RDKit #Memo”

Easy way to connect fragments #rdkit #tips #memo

I often use rxnSmarts to join fragments. In SMILES representation, each fragment is separated by dot ‘.’. An integer in the SMILES means connection of atoms. So by using the rule, it is easy to connect two fragmens. Here is an example of the rule. I learned the tips at RDKit UGM. It’s power ofContinue reading “Easy way to connect fragments #rdkit #tips #memo”

Install mdfptools #Chemoinformatics #RDKit #memo

I heard many exciting presentation at virtual meeting of ‘3rd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry’. And I had interest about MDFP (molecular dynamics Finger Print). MDFP can analyze molecular flexibility and solvent accessible surface are (SASA) etc. They are important parameters for permeability, p-gp and other molecular properties. In the following article combinationContinue reading “Install mdfptools #Chemoinformatics #RDKit #memo”

Lilly’s Chemoinformatics Tool Kit #memo #chemoinformatics

Almost 7 years ago, I posted a topics about Lilly’s MedChem filter which is disclosed on github. https://iwatobipen.wordpress.com/2013/08/06/lilly%E3%81%AE%E3%83%95%E3%82%A3%E3%83%AB%E3%82%BF/ It’s interesting for me because most of languages of code on Lilly’s repository are not python and C++, R etc. And one of interesting code is LillyMol. The licence of the code is Apache 2.0. I feltContinue reading “Lilly’s Chemoinformatics Tool Kit #memo #chemoinformatics”