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 conduct

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 The

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 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 and

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 dockdream