Doo Nam Kim's repositories
AF_Cluster
Predict multiple protein conformations using sequence clustering and AlphaFold2.
Ankh
Ankh: Optimized Protein Language Model
BioAutoMATED
Automated machine learning for analyzing, interpreting, and designing biological sequences
DiAMoNDBack
DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces
efficient-evolution
Efficient evolution from protein language models
evodiff
Generation of protein sequences and evolutionary alignments via discrete diffusion models
GENA_LM
GENA-LM is a transformer masked language model trained on human DNA sequence.
guide_bsasa
Buried Solvent Accessible Surface Area Calculations
miniforge
A conda-forge distribution.
numsa
Solvent accessible surface area calculation
openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
polnet
Generates synthetic datasets for Cryo-Electron Tomography
popsom
Population-based Self-Organizing Maps
Pose
A bare metal Python library for building and manipulating protein molecular structures
protpardelle
Diffusion-based all-atom protein generative model.
relion
Image-processing software for cryo-electron microscopy
ReprogBERT
Code for ICML 2023 paper "Reprogramming Pretrained Language Models for Antibody Sequence Infilling"
SaID
Official implementation of paper SaID for cryo-EM image denoising.
structuremap
Python package for investigating the structural context of PTMs
tempest
A ChimeraX plugin to visualize high-resolution template matching results from cisTEM
tomotwin-cryoet
cryo-ET particle picking using triplet networks and metric learning
wiggle
Graphical user interface to integrate cryoEM flexibility analyses with ChimeraX