Pinned Repositories
abodybuilder3
AF_Cluster
Predict multiple protein conformations using sequence clustering and AlphaFold2.
alphabind
AlphaBind code + model accompanying pre-print
alphafold
Open source code for AlphaFold.
ANARCI
Antibody Numbering and Antigen Receptor ClassIfication
AntiBERTy
Antibody-specific masked language model
BindCraft
User friendly and accurate binder design pipeline
boltz
Official repository for the Boltz-1 biomolecular interaction model
transformerCPI
TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524
transformerCPI2.0
Sequence-to-drug concept adds a perspective on drug design. It can serve as an alternative method to SBDD, particularly for proteins that do not yet have high-quality 3D structures available.
lifanchen-simm's Repositories
lifanchen-simm/abodybuilder3
lifanchen-simm/alphabind
AlphaBind code + model accompanying pre-print
lifanchen-simm/ANARCI
Antibody Numbering and Antigen Receptor ClassIfication
lifanchen-simm/BindCraft
User friendly and accurate binder design pipeline
lifanchen-simm/boltz
Official repository for the Boltz-1 biomolecular interaction model
lifanchen-simm/carbonmatrix_public
lifanchen-simm/chai-lab
Chai-1, SOTA model for biomolecular structure prediction
lifanchen-simm/chroma
A generative model for programmable protein design
lifanchen-simm/DynamicBind
repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
lifanchen-simm/ColabFold
Making Protein folding accessible to all!
lifanchen-simm/esm3
lifanchen-simm/evodiff
Generation of protein sequences and evolutionary alignments via discrete diffusion models
lifanchen-simm/EvolvePro
This is the offical codebase to reproduce and use EVOLVEpro, a model for in silico directed evolution of protein activities using few-shot active learning.
lifanchen-simm/GeoSeqBuilder
lifanchen-simm/HLAfreq
Aggregate HLA allele frequencies data from allelefrequencies.net at large multi population scale
lifanchen-simm/LigandMPNN
lifanchen-simm/MoCHI
Neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis and allostery from deep mutational scanning data
lifanchen-simm/MPB-EXP-MUT
lifanchen-simm/munis
lifanchen-simm/Pallatom
lifanchen-simm/PISTE
lifanchen-simm/PLACER
PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.
lifanchen-simm/PLTNUM
lifanchen-simm/protein_generator
Joint sequence and structure generation with RoseTTAFold sequence space diffusion
lifanchen-simm/ProteinMPNN
Code for the ProteinMPNN paper
lifanchen-simm/Protenix
A trainable PyTorch reproduction of AlphaFold 3.
lifanchen-simm/R-Drop
lifanchen-simm/RFdiffusion
Code for running RFdiffusion
lifanchen-simm/structural-evolution
lifanchen-simm/Uni-Mol
Official Repository for the Uni-Mol Series Methods