Large community software projects for molecular modeling that we use and contribute to in the lab
Rosetta is a platform for protein structure modeling and design. It is developed by dosens of labs and has a broad applications to sample and score protein conformations.
DOCK3.7 is designed for large-scale virtual screening of chemical libraries from ZINC15
A collection of tools to analyze Morphological Profiling experiments, which use high-throughput microsopy as readout for drug screens.
An R package for single-cell pharmacology
A python package for deep learning for microscopy and morphological profiling modeling
An R package to analyze high-throughput electrophysiology experiments including ex-vivo multi-electrode array and automated patch-clamp experimental setups
A set of R packages we have developed to for pharmacology analysis, drug-repurposing, hit-picking, and target-identification
An R package for modeling dose response experiments. It implements a principled Bayesian workflow building on brms and Stan.
Build and analyze co-expression networks for eukaryotic pathogens
Curate chemical and biological annotation datasets
Interact with the https://zinc15.docking.org, a webserver for commercially available compounds developed by the Irwin lab at UCSF.
Prepare and manage a UCSF Dock campaign using an opinionated organization
Interact with Manifold, a webserver developed for retrosynthesis prediction developed by PostERA.
Interact with the https://sea16.docking.org, a webserver to compute ligand similarity ensemble analysis developed by the Shoichet lab at UCSF.
Build and analyze multiple sequence alignments, phylogentic trees, and ancetral gene-reconstructions
A notebook based pipeline for the spatial phenotype analysis of crisp screens