carlocamilloni's Stars
rohitsinghlab/raygun
Template-based protein design with Raygun
compsciencelab/mdCATH
This repository houses all the scripts and notebooks utilized for generating, analyzing, and validating the mdCATH dataset. Some user examples are also available.
patrickbryant1/EvoBind
In silico directed evolution of peptide binders with AlphaFold
deepmodeling/Uni-Mol
Official Repository for the Uni-Mol Series Methods
moldyn/dcTMD
Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
aqlaboratory/genie2
Protein structure diffusion model for unconditional protein generation and motif scaffolding
aqlaboratory/openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
rdk/p2rank
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
bjing2016/alphaflow
AlphaFold Meets Flow Matching for Generating Protein Ensembles
zrqiao/NeuralPLexer
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
gcorso/DiffDock
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
baker-laboratory/rf_diffusion_all_atom
Public RFDiffusionAA repo
baker-laboratory/RoseTTAFold-All-Atom
dauparas/LigandMPNN
Profluent-Internships/MMDiff
Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion
AspirinCode/papers-for-molecular-design-using-DL
List of Molecular and Material design using Generative AI and Deep Learning
psf/black
The uncompromising Python code formatter
scanberg/viamd
Visual Interactive Analysis of Molecular Dynamics
multi-ego/multi-eGO
Set of tools to generate a multi-eGO force field to perform molecular dynamics simulations
aethertier/secstructartist
A python module to plot secondary structure schemes
cp2k/cp2k
Quantum chemistry and solid state physics software package
DessimozLab/fold_tree
snakemake pipeline for creating trees from sequence sets
luigibonati/mlcolvar
A unified framework for machine learning collective variables for enhanced sampling simulations
psipred/s4pred
A tool for accurate prediction of a protein's secondary structure from only it's amino acid sequence
uw-ipd/RoseTTAFold2
westpa/westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
jax-md/jax-md
Differentiable, Hardware Accelerated, Molecular Dynamics
RosettaCommons/RFdiffusion
Code for running RFdiffusion
sokrypton/RFdiffusion
Code for running RFdiffusion
openmm/openmm-plumed
OpenMM plugin to interface with PLUMED