Doo Nam Kim's repositories
alphascreen
Screen interactions with AlphaFold-Multimer
ArtiaX
ArtiaX is an open-source extension of the molecular visualisation program ChimeraX.
beta-lac-protein-design
Analysis scripts and data for the manuscript "Simultaneous Enhancement of Multiple Functional Properties Using Evolution-informed Protein Design"
blik
Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.
chimerax-trimmings
Useful aliases and startup settings for ChimeraX
CLEAN
CLEAN: a contrastive learning model for high-quality functional prediction of proteins
colabseg
Jupyter-based tool for membrane segmentation manipulation
CryoVesNet
segmentation of spherical vesicles in cryo-electron tomography
DeepDeWedge
Self-supervised deep learning for denoising and missing wedge reconstruction of cryo-ET tomograms
DiffModeler
DiffModeler: a diffusion model based protein complex structure modeling tool.
gms_natcomms_1705932980_data
Data sharing for High-throughput Prediction of Changes in Protein Conformational Distributions with Subsampled AlphaFold2
ImmuneBuilder
Predict the structure of immune receptor proteins
localcolabfold
ColabFold on your local PC
martini-workshop
Martini Workshop: Simulating a Minimal Bacterial Cell
membrain-seg
membrane segmentation in 3D for cryo-ET
NeuralPLexer
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
nglview
Jupyter widget to interactively view molecular structures and trajectories
PaddleHelix
Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集
pepmlm
Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling
PeptideBERT
Transformer Based Language Model for Peptide Property Prediction
PypKa
A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism
RoseTTAFold2NA
RoseTTAFold2 protein/nucleic acid complex prediction
SEQCROW
Plug-in for ChimeraX providing features for building and manipulating organic and organometallic molecules as well as displaying output from quantum chemistry computations.
TS2CG1.1
TS2CG version 1.1
unsup_cryoet
completion of missing wedge w unsupervised coordinate nets