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md-stateinterpreter

mdscan

An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics

minifold

MiniFold: Deep Learning for Protein Structure Prediction inspired by DeepMind AlphaFold algorithm

mol22lt

Perl script translating mol2 file to LAMMPS template file

monn

MONN: a Multi-Objective Neural Network for Predicting Pairwise Non-Covalent Interactions and Binding Affinities between Compounds and Proteins

mxfold2

MXfold2: RNA secondary structure prediction using deep learning with thermodynamic integration

onionnet-2

openfold

Trainable PyTorch reproduction of AlphaFold 2

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

peggenerator

Generate PEG topology for GROMACS and LAMMPS

plddt2csv

Extract the plddt value of Alphafold2 from .pkl to .csv file

prospr

ProSPr: Protein Structure Prediction

proteinmpnn

Code for the ProteinMPNN paper

pyautofep

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

python_zero

ゼロから学ぶPython

qeppi

Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions

radonpy

RadonPy is a Python library to automate physical property calculations for polymer informatics.

rgmolsa

surfmap

svgcollectionoflabequipment

SVG collection of lab equipment

teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data