biochunan
PhD student at UCL Computational Biology. Research focuses on developing deep learning tools for antibody development. Geometric Deep Learning, Protein LMs.
University College LondonLondon, UK
Pinned Repositories
3Dmol.js
WebGL accelerated JavaScript molecular graphics library
ab-docking-scripts
absplit
Code to split an antibody PDB file into Fv fragments with their antigens
AsEP-dataset
NeurIPS 2024 Dataset and Benchmark Submission "AsEP: Benchmarking Deep Learning Methods for Antibody-specific Epitope Prediction"
CDRConformationClassification
Antibody CDR loop conformation clusteirng using Affinity Propagation
Convert2vscSnippet
a simple shell script to convert a piece of code to vscode snippet
esmfold-docker-image
Create a docker image for running ESMFold, solved conflicts between ESMFold and OpenFold dependencies
find_contacts_pymol_plugin
A PyMOL plugin to visualize interface residues
graphein
Protein Graph Library
seqres2atmseq
Align the SEQRES sequence with the ATMSEQ sequence of a protein chain and output a list of mask (0: a missing residue in the ATMSEQ; 1: match)
biochunan's Repositories
biochunan/AsEP-dataset
NeurIPS 2024 Dataset and Benchmark Submission "AsEP: Benchmarking Deep Learning Methods for Antibody-specific Epitope Prediction"
biochunan/esmfold-docker-image
Create a docker image for running ESMFold, solved conflicts between ESMFold and OpenFold dependencies
biochunan/find_contacts_pymol_plugin
A PyMOL plugin to visualize interface residues
biochunan/ab-docking-scripts
biochunan/abdockgen
biochunan/alphafold
Open source code for AlphaFold.
biochunan/Convert2vscSnippet
a simple shell script to convert a piece of code to vscode snippet
biochunan/graphein
Protein Graph Library
biochunan/alphaflow
AlphaFold Meets Flow Matching for Generating Protein Ensembles
biochunan/alphafold3
AlphaFold 3 inference pipeline.
biochunan/bio-datasets
Bringing bio (molecules and more) to the huggingface datasets library
biochunan/biochunan
biochunan/BiomedGPT
BiomedGPT: A Generalist Vision-Language Foundation Model for Diverse Biomedical Tasks
biochunan/chai-lab
Chai-1, SOTA model for biomolecular structure prediction
biochunan/chunan.github.io
biochunan/DiffAbXL
The official implementation of DiffAbXL benchmarked in the paper "Exploring Log-Likelihood Scores for Ranking Antibody Sequence Designs", formerly titled "Benchmarking Generative Models for Antibody Design".
biochunan/DiffDock-PP
Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
biochunan/FoldFlow
FoldFlow: SE(3)-Stochastic Flow Matching for Protein Backbone Generation
biochunan/GCPNet
A PyTorch implementation of Geometry-Complete SE(3)-Equivariant Perceptron Networks (GCPNets)
biochunan/GCPNet-EMA
Protein Structure Accuracy Estimation using Geometry-Complete Perceptron Networks (Protein Science 2024)
biochunan/Graphormer
Graphormer is a general-purpose deep learning backbone for molecular modeling.
biochunan/HEAL
biochunan/KRAGEN
Software to implement GoT with a weviate vectorized database
biochunan/mdgen
Generative modeling of molecular dynamics trajectories
biochunan/neo4j-app-python
https://graphacademy.neo4j.com/courses/app-python
biochunan/openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
biochunan/pinder
PINDER: The Protein INteraction Dataset and Evaluation Resource
biochunan/ProteinWorkshop
Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)
biochunan/RFantibody
biochunan/RFdiffusion
Code for running RFdiffusion