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perses

Experiments with expanded ensembles to explore chemical space

pesto

pf-gnn_pli

pigvae

pka-ani

Accurate prediction of protein pKa with representation learning

plumed-westpa

plumed-with-amber-and-gromacs

In this pdf file i have wrote down the important steps for installing of plumed , gromacs nad amber and patching the PLUMED with other MD engines. This may not work for everyone but i believe it will work for most of the persons

plumed_scripts

pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

pointvs

SE(3)-equivariant point cloud networks for virtual screening

polyply_regression_tests

Regression tests and tutorial input files for the polyply software suite

postmetad

Python package for post-processing PLUMED metadynamics and OPES simulations.

practicalsessions2021

proteinmpnn

Code for the ProteinMPNN paper

pyautofep

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

pybinde

Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations in protein-protein and protein-ligand systems

pyemma-workshop

pypdb

A Python API for the RCSB Protein Data Bank (PDB)

pytorch

Deep Learning Zero to All - Pytorch

pytorch-optimizer

torch-optimizer -- collection of optimizers for Pytorch

pytorch_geometric

Graph Neural Network Library for PyTorch

pytorch_geometric_signed_directed

PyTorch Geometric Signed Directed is a signed/directed graph neural network extension library for PyTorch Geometric.

pytorch_geometric_temporal

PyTorch Geometric Temporal: Spatiotemporal Signal Processing with Neural Machine Learning Models (CIKM 2021)

pytorchgeometrictutorial

Pytorch Geometric Tutorials

quicksom

realvs

Reproducing of the paper entitled "RealVS: Towards Enhancing the Precision of Top Hits in Ligand-Based Virtual Screening of Drug Leads from Large Compound Databases" (Journal of Chemical Information and Modeling)

reform

A simple implementation of replica exchange MD simulations for OpenMM.

remd-scheduler

Computes the optimum temperatures to use in an REMD simulation.

reweight

Reimplementation of aMD reweighting protocol

saltswap

Package to fluctuate the number of counterions in an OpenMM simulation