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accelerated_sampling_with_autoencoder

Accelerated sampling framework with autoencoder-based method

advligprep

Parmed based python program for preparing TI parm7

alphaflow

AlphaFold Meets Flow Matching for Generating Protein Ensembles

awesome-community-detection

A curated list of community detection research papers with implementations.

bioinfokit

Bioinformatics data analysis and visualization toolkit

biopython

Official git repository for Biopython (originally converted from CVS)

cookiecutter-cms

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

csa

Python implementation of conformational space annealing

d3r-gc4

data from D3R Grand Challenge 4 2018

dbda-python

Doing Bayesian Data Analysis, 2nd Edition (Kruschke, 2015): Python/PyMC3 code

discrete-shocklet-transform

Forked from https://gitlab.com/compstorylab/discrete-shocklet-transform

edward

A probabilistic programming language in TensorFlow. Deep generative models, variational inference.

ensembler

geometric-gnn-dojo

Geometric GNN Dojo provides unified implementations and experiments to explore the design space of Geometric Graph Neural Networks.

lica

The Python version of the least dependent component analysis and mutual information methods proposed by A. Kraskov, H. Stögbauer, and P. Grassberger, Phys. Rev. E 69 (6) 066138, 2004.

linear_programming

loos

LOOS: a lightweight object-oriented structure analysis library

map_align

Contact map alignment

md_membrane_proteins

Scripts for removing water molecules of membrane-proteins in AMBER PDB format. Various MD data analysis scripts.

mdtraj

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

network_clustering

Python scripts used for DREAM11: Module disease identification

piny

PINY cleanup and new feature integration.

plumed2

Development version of plumed 2

pnerf

proteinmpnn

Code for the ProteinMPNN paper

pyxmeans

Quick implementation of xmeans in python and C

ramd-analysis

scripts to analyze NAMD trajectories generated by RAMD

reassigner

This software reads pdb files (or downloads them from the web) and assigns secondary structure.

scripts-distance-fluctuations

Calculates distance fluctuations of atoms from long MD trajectories

sss-drawer

Simple python script to visualise secondary structures as a single SVG image.