Pinned Repositories
3D-Generative-SBDD
💊 A 3D Generative Model for Structure-Based Drug Design (NeurIPS 2021)
_2022_ML-ddG-Blaabjerg
ab-ag-seq-machine-learning
ab-gen
ab_opt
Official implementation of Generative Diffusion Models for Antibody Design, Docking, and Optimization.
ab_rmsd
Calculate the RMSD between two antibody structure (including nanobody and antibody).
AbDev
abdockgen
AbFlex
RFDesign
Protein hallucination and inpainting with RoseTTAFold
kehan777's Repositories
kehan777/_2022_ML-ddG-Blaabjerg
kehan777/AGAT-PPIS
AGAT-PPIS is a protein-protein interaction site predictor based on deep graph neural networks.
kehan777/AlphaFold-disorder
Predict disorder and disorder binding from AlphaFold structures
kehan777/APPRAISE
Rank binders by structure modeling
kehan777/ASGARD
ASGARD is a tool that allows via an automated MD workflow to perform MD protein or protein-ligand complex analysis and to generate the corresponding report easily
kehan777/AttnPacker
Code and Pre-Trained Models for "AttnPacker: An end-to-end deep learning method for protein side-chain packing"
kehan777/ColabDesign
Making Protein Design accessible to all via Google Colab!
kehan777/DDGScan
DDGScan: an integrated parallel workflow for the in silico point mutation scan of protein
kehan777/DiffDock-PP
Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
kehan777/DuIvyTools
A Tool to process the result files of GMX MD.
kehan777/EigenFold
EigenFold: Generative Protein Structure Prediction with Diffusion Models
kehan777/fftw3
DO NOT CHECK OUT THESE FILES FROM GITHUB UNLESS YOU KNOW WHAT YOU ARE DOING. (See below.)
kehan777/gamd-openmm
Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth the potential energy surface and reduce system energy barriers. http://miao.compbio.ku.edu/GaMD/
kehan777/GeoStab
kehan777/gmx_MMPBSA
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
kehan777/gmxtools
tools for GROMACS
kehan777/Graphormer
Graphormer is a deep learning package that allows researchers and developers to train custom models for molecule modeling tasks. It aims to accelerate the research and application in AI for molecule science, such as material design, drug discovery, etc.
kehan777/HIGH-PPI
kehan777/icor-codon-optimization
RNN-based Codon Optimization Tool. Publication: https://doi.org/10.1186/s12859-023-05246-8
kehan777/kasearch
KA-Search: Rapid and exhaustive sequence identity search of known antibodies
kehan777/korpm
Predicting the effect of mutations on protein stability using a simple orientational potential.
kehan777/libzeep
C++ library for reading and writing XML and creating web and SOAP servers
kehan777/LinearDesign
The LinearDesign mRNA design software.
kehan777/nab-seq
Code for NAb-Seq manuscript
kehan777/OpenComplex
Trainable PyTorch framework for developing protein, RNA and complex models.
kehan777/protocolGromacs
Automatic gromacs protocol from preparation to production with ligand parametrization through
kehan777/RaptorX-Single
kehan777/RESP
The code used to generate the results from Parkinson / Hard et al. 2022
kehan777/uASPIre_UTR_CDS
Data and code of the paper "Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript"
kehan777/visualdynamics
Web Platform made with Python for automatic GROMACS simulations