Pinned Repositories
100-Days-Of-ML-Code
100 Days of ML Coding
2019-smORF
Scripts to identify small open reading frames using ribosome profiling data
af2complex
Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
bio-pipeline
My collection of light bioinformatics analysis pipelines for specific tasks
DupGen_finder
A pipeline used to identify different modes of duplicated gene pairs
FunGAP
FunGAP: fungal Genome Annotation Pipeline
Liftoff
An accurate GFF3/GTF lift over pipeline
qvina
Accurately speed up AutoDock Vina
ribotricer
A tool for accurately detecting actively translating ORFs from Ribo-seq data
scripts-for-SSR-project
128 Phytophthora Isolates Reveal Species-Specific Microsatellite Distribution
biogeeker's Repositories
biogeeker/AI2BMD
AI-powered ab initio biomolecular dynamics simulation
biogeeker/ASTRAL
Accurate Species TRee ALgorithm
biogeeker/CLEAN
CLEAN: a contrastive learning model for high-quality functional prediction of proteins
biogeeker/codon-bias
Python package of codon usage bias analysis tools
biogeeker/ColabDesign
Making Protein Design accessible to all via Google Colab!
biogeeker/deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
biogeeker/DeepPurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
biogeeker/DeepRank-GNN-esm
Graph Network for protein-protein interface including language model features
biogeeker/efficient-evolution
Efficient evolution from protein language models
biogeeker/evolution
This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'
biogeeker/External-Attention-pytorch
🍀 Pytorch implementation of various Attention Mechanisms, MLP, Re-parameter, Convolution, which is helpful to further understand papers.⭐⭐⭐
biogeeker/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.
biogeeker/gmxtools
tools for GROMACS
biogeeker/gnina
A deep learning framework for molecular docking
biogeeker/nf-anvio-pangenome
Analyze a set of genomes with the anvi'o pangenome pipeline
biogeeker/OpenFermion
The electronic structure package for quantum computers.
biogeeker/piston
Evaluating Protein Binding Interfaces with Transformer Networks
biogeeker/prompt2model
prompt2model - Generate Deployable Models from Natural Language Instructions
biogeeker/protein_bert
biogeeker/protein_seq_des
Code for our paper "Protein sequence design with a learned potential"
biogeeker/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.
biogeeker/PyAutoFEP
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
biogeeker/pyGenomeViz
A genome visualization python package for comparative genomics
biogeeker/QSproteome_protocol
contains all the necessary script and data to calculate everything from input pdb model + json file to dimer probability
biogeeker/RFdiffusion
Code for running RFdiffusion
biogeeker/RoseTTAFold2NA
RoseTTAFold2 protein/nucleic acid complex prediction
biogeeker/TADbit
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data.
biogeeker/Uni-GBSA
An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.
biogeeker/UTR-LM
biogeeker/zotero-addons
Zotero add-on to list and install add-ons in Zotero