Recently I think relationship between ML and CADD become more closer compared to several years ago. DiffDock is one of the very nice work for interation of cheminformatics and SBDD. It uses diffusion model for protein-ligand pose prediction. But DiffDock can’t run constrain docking which define specific location of protein pocket. Also pure docking toolContinue reading “New Diffusion model based docking tool #MolSnapper #cheminformatics #RDKit”
Tag Archives: SBDD
Use DiffDock as web application #DiffDock #cheminformatics #memo
As many readers know that DiffDock is one of the famous Deep Learning based docking program which use diffusion model. It was published 2022 at arxiv and code is disclosed on github. Recenlty I found that the repository was updated and code for web application is added :)https://github.com/gcorso/DiffDock I interested it because web app isContinue reading “Use DiffDock as web application #DiffDock #cheminformatics #memo”
Try to make SBDD work flow with Flow Based Programming(FBP) #cheminformatics #SBDD #RDKit #python
If target structure of the drug discovery project is available, SBDD is one of the practical approach. Docking study is common method of SBDD. There are lots of docking simulation softwares recently not only commercial packages but also open source software. AutoDock Vina is one of the famous Docking tool in the area. To runContinue reading “Try to make SBDD work flow with Flow Based Programming(FBP) #cheminformatics #SBDD #RDKit #python”
Pocket awaer structure generation #DiffDec #cheminformatics
Diffusion model is the one of hot area of generative model. It’s not only computer vision but also cheminformatics. Diffusion model is interesting because it generates object from some noise. BTW, de novo compound design with target protein structure information is really attractive but difficult approach in drug design. There are some approaches to conductContinue reading “Pocket awaer structure generation #DiffDec #cheminformatics”
Run Autodock Vina on Batch mode #Vina #memo
As most of readers know that autodock vina is one of the famous open source docking tool. So users can run virtual screening on theire own PC ;) If there are many ligands to dock, some code is required to run the dock, for example following shell script is provided from original site. https://vina.scripps.edu/manual/#screening TheContinue reading “Run Autodock Vina on Batch mode #Vina #memo”
Run virtual screening with only python! #chemoinformatics #SBDD
If you have protein-ligand co- crystal structure at the early stage of drug discovery, SBDD based approach is useful I think. As many readers know that there are lots of useful commercial packages to conduct SBDD. But also there are useful packages at Open science area. One of the famous and useful OSS for SBDDContinue reading “Run virtual screening with only python! #chemoinformatics #SBDD”
Make mdtools for openmm #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”
Reinforcement learning with docking score #RDKit #reinvent #chemoinforamtics
Previously I posted automated docking system called dockstream. It supports many compound-protein docking software and recent version of reinvent supports dockstream as scoring method. From the dockstream documentation, reinvent v3.0 supports dockstream but it didn’t work due to some issue of reinvent-scoring which manage scoring function of reinvent. I modified source code to use dockdreamContinue reading “Reinforcement learning with docking score #RDKit #reinvent #chemoinforamtics”
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