JacobKMcPherson
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Scientific programming
an interactive viewer for populations of bacterial genomes linked by a phylogeny
Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://d…
MMseqs2: ultra fast and sensitive search and clustering suite
functions to analyse sanger sequencing reads in R
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
a deep learning architecture for protein-ligand binding affinity prediction
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
MDAnalysis is a Python library to analyze molecular dynamics simulations.
A companion R package for the MicrobiomeAnalyst web server
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2
This package contains deep learning models and related scripts for RoseTTAFold
RoseTTAFold2 protein/nucleic acid complex prediction
Infrastructure template and Jupyter notebooks for running RoseTTAFold on AWS Batch.
Binder, tool for automatic generation of Python bindings
ChEMBL database structure pipelines
AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the mod…
Deep learning for molecules and materials book
An easy-to-use, flexible website template for labs.
A collaboratively written review paper on deep learning, genomics, and precision medicine
Conda recipes for the bioconda channel.
MMseqs2 app to run on your workstation or servers