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/AFM-LIS
Local Interaction Score (LIS) Calculation from AlphaFold-Multimer (Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer)
kimdn/Ais
kimdn/alphabind
kimdn/alphafold3
AlphaFold 3 inference pipeline.
kimdn/AlphaPulldown
kimdn/bionumpy
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
kimdn/chai-lab
Chai-1, SOTA model for biomolecular structure prediction
kimdn/cisTEM
kimdn/concerto
kimdn/Cryo2Struct
Deep learning tools for converting cryo-EM density maps to protein structures
kimdn/deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
kimdn/foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
kimdn/GRACE
GRACE: Generative Renaissance in Artificial Computational Enzyme Design
kimdn/Graphormer
Graphormer is a general-purpose deep learning backbone for molecular modeling.
kimdn/haddock3
Official repo of the modular BioExcel version of HADDOCK
kimdn/heme_binder_diffusion
kimdn/IgLM
Generative Language Modeling for Antibody Design
kimdn/imodmodel
IMOD model files as pandas dataframes in Python
kimdn/LigandMPNN
kimdn/localcolabfold
ColabFold on your local PC
kimdn/mdgen
kimdn/Meeko
Interfacing RDKit and AutoDock
kimdn/membrain-pick
kimdn/ncap
kimdn/Protenix
A trainable PyTorch reproduction of AlphaFold 3.
kimdn/pytom-match-pick
GPU-accelerated template matching for cryo-ET
kimdn/rf_diffusion_all_atom
Public RFDiffusionAA repo
kimdn/STOPGAP
STOPGAP is a MATLAB-based package for subtomogram averaging.
kimdn/TARDIS
Transformer And Rapid Dimensionless Instance Segmentation
kimdn/tomoProcess
Scripts used for EMSL tomography data processing