mihirdate's repositories
awesome-molecular-generation
Awesome papers related to generative molecular modeling and design.
deep-molecular-optimization
Molecular optimization by capturing chemist’s intuition using the Seq2Seq with attention and the Transformer
DiffDock
Colab version of "DiffDock: : Diffusion Steps, Twists, and Turns for Molecular Docking"
DiffDock-original
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
GraphINVENT
Graph neural networks for molecular design.
kinase_msm
set of scripts to analyze kinases
mdtraj
An open library for the analysis of molecular dynamics trajectories
MEAD
Macroscopic Electrostatics with Atomic Detail
MEAD_2.2.9
A copy of MEAD v. 2.2.9 (Macroscopic Electrostatics with Atomic Detail) by Donald Bashford (released by the author under GPL v.1)
ML_MD_utility_codes
Different utility codes for MD and ML
MSMs
Markov state models
NeuralForceField
Neural Network Force Field based on PyTorch
novana
Novana is a cheminformatics tool that allows decomposing molecules into their scaffolds and shapes.
openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Pocket2Mol
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
pysmilesutils
Utilities for working with SMILES based encodings of molecules for deep learning (PyTorch oriented)
RAVE
Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)
Siamese-RNN-Self-Attention
Contains code for Siamese Recurrent Neural Network with Self-Attention for Bioactivity Prediction
smi2sdf
Conversion of SMILES to SDF files through RDKit
Uni-Fold
An open-source platform for developing protein models beyond AlphaFold.