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openmm-tutorials

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

openmm-validation

[Work in progress] An extensive validation suite for the OpenMM molecular simulation library.

openmmenergycomparisons

Comparisons of energies and forces between OpenMM and other packages

openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

pdb-analysis

A simple python script to extract the "phi/psi" torsion angles for a protein data bank file.

pdbanalyzer

PDB Metal Stats

pdbanalyzer-results

Results of PDB-wide metal analyses

pdbfinder

a collection of scripts and files to help in PDB retrieval for various projects

peanut

pesscan

A python script for generating configurations in simple potential energy surface scans

pgmpy

Python Library for learning (Structure and Parameter) and inference (Statistical and Causal) in Bayesian Networks.

pgmpy-modified

Modificação da Bioblioteca implementada em python Pgmpy, adicionando alguns recursos como Redes Bayesianas Dinâmicas e adição de conhecimento biológico a priori nas funções de pontuação BIC e BDeu.

pgmpy_notebook

Short Tutorial to Probabilistic Graphical Models(PGM) and pgmpy

pmi

Python Modeling Interface

preanalrot

A toy pdb reader, analyzer, and bond rotater

proteinfoldingpipeline

Pipeline for protein folding using distance and torsion restraints from an amino acid sequence; AmberTools18 wrapped in Python

protons

OpenMM testbed for constant-pH methodologies.

protons-templates

Templates for running protons simulations

provis

Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."

pygsm

Thermal and photochemical reaction path optimization and discovery

pyhessian

PyHessian is a Pytorch library for second-order based analysis and training of Neural Networks

pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

pyxtal

A code to generate crystal structure

qmmm-hydration

QM/MM hydration free energy playground

reaction_prediction_seq2seq

reactivity-ml-data

datasets to accompany the paper "What does the machine learn? Knowledge representations of chemical reactivity"

registers

A Data Package which is a database of public and private registers of clinical trials.

ring-open-fep

Ring-opening strategy for FEP.

rmsd-gradients

Fast gradients for receptor-ligand RMSD

rocsalt

Dual topology alchemical free energies