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2019-ncov

Network-based Drug Repurposing for Human Coronavirus

acemd-plumed

Running biased simulations with PLUMED and ACEMD

allopred

Predict allosteric pockets on proteins

amber-maestro-lipid-tutorial

Tutorial to build AMBER compatable protein+lipid systems

anharmonic.net

Anharmonic conformational analysis (ANCA)

bm5-clean

Docking benchmark 5 - cleaned and ready to use for HADDOCK

chap

CHAP is a tool for the functional annotation of ion channel structures:

ddmd

Local implementation of DeepDriveMD

dxtuber

entk_cvae_md

A script that runs Molecular Dynamics simulations under supervision of Machine Learning model on Summit@ORNL through Radical toolkit.

fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).

gsatools

Analysis of allosteric communication and functional local motions using a structural alphabet

hh-suite

Remote protein homology detection suite.

htmd

HTMD: Programming Environment for Molecular Discovery

illustrate

Biomolecular Illustration Tool

ivis

Dimensionality reduction in very large datasets using Siamese Networks

ivis_dimensionality-reduction_via_siamese-networks

A notebook benchmarking a recently developed Dimensionality Reduction technique using Siamese Networks supporting both supervised and unsupervised modes.

matplotlib

matplotlib: plotting with Python

matplotlib-gallery

Examples of matplotlib codes and plots

matplotlib-tutorial

Matplotlib tutorial for beginner

md-task

Tool suite for analysing molecular dynamics trajectories using network analysis and PRS

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

mdentropy

Analyze correlated motions in MD trajectories with only a few lines of Python.

mdplot

MDplot: Visualise Molecular Dynamics

mdsrv

MD trajectory server

mdtraj

A modern, open library for the analysis of molecular dynamics trajectories

molstar

A comprehensive macromolecular library

msmbuilder

:building_construction: Statistical models for biomolecular dynamics :building_construction:

msmbuilder2022

Statistical models for biomolecular dynamics

msmexplorer

Data visualizations for biomolecular dynamics