Pinned Repositories
cryo_fit
cryo_fit1 source codes, test files, live at .../phenix-xxxx/modules
cryo_fit2
cryo_fit2 source codes, test files, live at .../phenix-xxxx/modules
3D-VQ-VAE-2
3D VQ-VAE-2 for high-resolution CT scan synthesis
3D_Scaffold
3DShape2VecSet
4D-CHAINS
4D-CHAINS software for protein NMR assignment
a-cnn
adaptivediffgrid_ex
AutoMicroED
kimdn's Repositories
kimdn/adaptivediffgrid_ex
kimdn/AF_Cluster
Predict multiple protein conformations using sequence clustering and AlphaFold2.
kimdn/Ankh
Ankh: Optimized Protein Language Model
kimdn/BioAutoMATED
Automated machine learning for analyzing, interpreting, and designing biological sequences
kimdn/CP_tutorial
Introduction to cyclic peptide simulations and our group's protocols.
kimdn/cryosieve
kimdn/CST_Prop_Opt_ML
kimdn/DeepETPicker
kimdn/DiAMoNDBack
DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces
kimdn/DynaMight
Tool for reconstruction and analysis of continuous heterogeneity of a cryo-EM dataset
kimdn/evodiff
Generation of protein sequences and evolutionary alignments via discrete diffusion models
kimdn/GENA_LM
GENA-LM is a transformer masked language model trained on human DNA sequence.
kimdn/guide_bsasa
Buried Solvent Accessible Surface Area Calculations
kimdn/miniforge
A conda-forge distribution.
kimdn/numsa
Solvent accessible surface area calculation
kimdn/OccuPy
kimdn/openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
kimdn/polnet
Generates synthetic datasets for Cryo-Electron Tomography
kimdn/popsom
Population-based Self-Organizing Maps
kimdn/Pose
A bare metal Python library for building and manipulating protein molecular structures
kimdn/protpardelle
Diffusion-based all-atom protein generative model.
kimdn/PTMPSI
kimdn/recovar
kimdn/relion
Image-processing software for cryo-electron microscopy
kimdn/ReprogBERT
Code for ICML 2023 paper "Reprogramming Pretrained Language Models for Antibody Sequence Infilling"
kimdn/SaID
Official implementation of paper SaID for cryo-EM image denoising.
kimdn/structuremap
Python package for investigating the structural context of PTMs
kimdn/tempest
A ChimeraX plugin to visualize high-resolution template matching results from cisTEM
kimdn/tomotwin-cryoet
cryo-ET particle picking using triplet networks and metric learning
kimdn/wiggle
Graphical user interface to integrate cryoEM flexibility analyses with ChimeraX