AspirinCode

ColabFold

Making Protein folding accessible to all!

esm

PyxLSTM

Efficient Python library for Extended LSTM with exponential gating, memory mixing, and matrix memory for superior sequence modeling.

af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

OAReactDiff

An object-aware diffusion model for generating chemical reactions

MD-IFP

MD trajectory analysis using protein-ligand Interaction Fingerprints

PoseBench

Comprehensive benchmarking of protein-ligand structure generation methods (ICML 2024 AI4Science)

EternaFold

Improving RNA structure prediction through multitask learning on diverse crowdsourced data.

AFsample2

Modelling protein conformational landscape with Alphafold

vde_metadynamics

Enhanced protein mutational sampling using time-lagged variational autoencoders

Graph2Edits

spmm

Multimodal learning for chemical domain, with SMILES and properties.

gtalign_alpha

GTalign, HPC protein structure alignment, superposition and search (alpha release)

dgram2dmap

Converts AlphaFold distograms into distance matrices and saves them into a number of formats

ChiENN

AlphaTraj

Pocket dynamics analysis tool

MoleculeDiffusionGAN

WIP implementation of a discriminator-guided diffusion model for molecule generation.

2024-sbdd-benchmark

AlphaFold3_Result_Visualize

A convinent tool to visualize AlphaFold 3 prediction results with PyMOL and matplotlib

MD-trajectory_analysis

Tools for analysis of Molecular Dynamics trajectories (based on the MDAnalysis and RDKit libraries)

md_trajectory_analysis

Use MDAnalysis to calculate RDF and CDF

sbdd_practical_evaluation

From Theory to Therapy: Reframing SBDD Model Evaluation via Practical Metrics

FRETrest

Helper scripts for FRET-restrained MD simulations. Generate AMBER restraint files (DISANG).

open_source_deep_docking_protocol

Open Source Deep Docking protocol (optimized)

amberGaMD

GaMD patched amber

frameanalysis

Trajectory analysis for residue pairs build in MDAnalysis

REMD

Replica Exchange Molecular Dynamics for Peptides Aggregation

protein_antibody_interface_design_platform

2024-02-PK-parameters-visualized

postresql-rdkit-build

memo for building cartridge