biogeeker's repositories
AI2BMD
AI-powered ab initio biomolecular dynamics simulation
ASTRAL
Accurate Species TRee ALgorithm
CLEAN
CLEAN: a contrastive learning model for high-quality functional prediction of proteins
ColabDesign
Making Protein Design accessible to all via Google Colab!
deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
DeepPurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
DeepRank-GNN-esm
Graph Network for protein-protein interface including language model features
efficient-evolution
Efficient evolution from protein language models
evolution
This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'
External-Attention-pytorch
🍀 Pytorch implementation of various Attention Mechanisms, MLP, Re-parameter, Convolution, which is helpful to further understand papers.⭐⭐⭐
gmx_MMPBSA
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
gmxtools
tools for GROMACS
gnina
A deep learning framework for molecular docking
iSeq
Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
nf-anvio-pangenome
Analyze a set of genomes with the anvi'o pangenome pipeline
OpenFermion
The electronic structure package for quantum computers.
piston
Evaluating Protein Binding Interfaces with Transformer Networks
prompt2model
prompt2model - Generate Deployable Models from Natural Language Instructions
protein_seq_des
Code for our paper "Protein sequence design with a learned potential"
ProtTrans
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
PyAutoFEP
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
pyGenomeViz
A genome visualization python package for comparative genomics
QSproteome_protocol
contains all the necessary script and data to calculate everything from input pdb model + json file to dimer probability
RFdiffusion
Code for running RFdiffusion
RoseTTAFold2NA
RoseTTAFold2 protein/nucleic acid complex prediction
TADbit
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data.
Uni-GBSA
An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.
zotero-addons
Zotero add-on to list and install add-ons in Zotero