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/AlphaPulldown
kimdn/alphascreen
Screen interactions with AlphaFold-Multimer
kimdn/ArtiaX
ArtiaX is an open-source extension of the molecular visualisation program ChimeraX.
kimdn/beta-lac-protein-design
Analysis scripts and data for the manuscript "Simultaneous Enhancement of Multiple Functional Properties Using Evolution-informed Protein Design"
kimdn/blik
Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.
kimdn/chai-lab
Chai-1, SOTA model for biomolecular structure prediction
kimdn/cisTEM
kimdn/CLEAN-Contact
PyTorch Implementation of CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference
kimdn/colabseg
Jupyter-based tool for membrane segmentation manipulation
kimdn/CryoVesNet
segmentation of spherical vesicles in cryo-electron tomography
kimdn/DeepDeWedge
Self-supervised deep learning for denoising and missing wedge reconstruction of cryo-ET tomograms
kimdn/drgnai
kimdn/foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
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/HighFold
kimdn/LigandMPNN
kimdn/localcolabfold
ColabFold on your local PC
kimdn/martini-workshop
Martini Workshop: Simulating a Minimal Bacterial Cell
kimdn/Meeko
Interfacing RDKit and AutoDock
kimdn/membrain-pick
kimdn/membrain-seg
membrane segmentation in 3D for cryo-ET
kimdn/Protein_Redesign
Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models
kimdn/pytom-match-pick
GPU-accelerated template matching for cryo-ET
kimdn/rf_diffusion_all_atom
Public RFDiffusionAA repo
kimdn/SEQCROW
Plug-in for ChimeraX providing features for building and manipulating organic and organometallic molecules as well as displaying output from quantum chemistry computations.
kimdn/STOPGAP
STOPGAP is a MATLAB-based package for subtomogram averaging.
kimdn/ThermoMPNN
GNN trained to predict changes in thermodynamic stability for protein point mutants
kimdn/tomoProcess
Scripts used for EMSL tomography data processing