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af-cryptic-pocket

Cryptic pocket prediction using AlphaFold 2

af2_conformations

A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2

ai-de-novo-molecule-design

Deep learning AI for generating new molecules that bond to the COVID-19.

alphafold

Open source code for AlphaFold.

ann_sampling

Learning free energy landscapes using artificial neural networks

awesome-small-molecule-ml

A curated list of resources for machine learning for small-molecule drug discovery

aws-graviton-md-example

Helping MD customers run workloads on Graviton 3E instances (especially hpc7g) with optimized compiler settings

bayesian-flow-networks

This is the official code release for Bayesian Flow Networks.

bio-sfa

Code for reproducing the experiment from the paper "A biologically plausible neural network for Slow Feature Analysis"

bpti-tica-waterdynamics

tICA to capture local loop motion. Describes how to analyse loop movement using TICA and how to run PT-Metad using TIC vectors

char-rnn.pytorch

PyTorch implementation of char-rnn (character-level language model)

classifier-cv-sampling

Binary classifier as CV in enhanced sampling

clustergcn

A PyTorch implementation of "Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks" (KDD 2019).

colvar

A package that allows you to read COLVAR output from Plumed and access data

compressionvae

General-purpose dimensionality reduction and manifold learning tool based on Variational Autoencoder, implemented in TensorFlow.

covid-moonshot

Scripts and input files associated with docking and free energy calculations for the COVID Moonshot

d3-hlp-msm-workflow

MSM workflow for: Thomas, T.; Yuriev, E; Chalmers, D. K. "MarkovState Model Analysis of Haloperidol Binding to the D3 Dopamine Receptor."

debasmita-das-econ.github.io

This is a repository of my website.

deepinfomaxpytorch

Learning deep representations by mutual information estimation and maximization

diffdock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

diffusionproteinligand

dim

Deep InfoMax (DIM), or "Learning Deep Representations by Mutual Information Estimation and Maximization"

dsfanet

[TGRS 2019] Unsupervised Deep Slow Feature Analysis for Change Detection in Multi-Temporal Remote Sensing Images

euporie

Jupyter notebooks in the terminal

exposons-with-jug

Use the parallelization framework jug to build exposons!

fah-alchemy

protein-ligand alchemical free energy calculations via Folding@Home

flareplot

Visualization tool for changing networks

fmap_v1

Codes to use funnel-metadynamics and funnel metadynamics automated protocol

frame-flow

Fast protein backbone generation with SE(3) flow matching.

funnel-metadynamics

This repo is designed to give initial files to perform Funnel metadynamics as described in the paper Resolving the problem of trapped water in binding cavities: prediction of host–guest binding free energies in the SAMPL5 challenge by funnel metadynamics (https://link.springer.com/article/10.1007/s10822-016-9948-6)