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programmingassignment2

Repository for Programming Assignment 2 for R Programming on Coursera

prolif

Protein-Ligand Interaction Fingerprints

prolif-1

Protein-Ligand Interaction Fingerprints

propka-3.1

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

protac-rl

protocaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS

psearch

3D ligand-based pharmacophore modeling

psi4

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

psikit

psi4+RDKit

ptools

pubchempy

Python wrapper for the PubChem PUG REST API.

pychembldb

chembldb for python

pycontact

Analysis of non-covalent interactions in MD trajectories

pydhamed

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations

pyheat

pprofile + matplotlib = Python program profiled as an awesome heatmap!

pymol-color-alphafold

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

pynamd

Python Tools for NAMD

pyproct

pyProCT is an open source cluster analysis software especially adapted for jobs related with structural proteomics. Its approach allows users to define a clustering goal (clustering hypothesis) based on their domain knowledge. This hypothesis will guide the software in order to find the best algorithm and parameters (including the number of clusters) to obtain the result that fulfills their expectatives. In this way users do not need to use cluster analysis algorithms as a black box, improving this way the results. pyProCT not only generates a resulting clustering, it also implements some use cases like the extraction of representatives or trajectory redundance elimination.

pyrosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

pyscreener

pythonic interface to virtual screening software

pyseqm

an interface to semi-empirical quantum chemistry methods implemented with pytorch

python-feature-engineering-cookbook

Python Feature Engineering Cookbook, published by Packt

python-gui-programming-cookbook-second-edition

Python GUI Programming Cookbook, Second Edition, published by Packt

python-guide

Python best practices guidebook, written for Humans.

python-machine-learning-book-2nd-edition

The "Python Machine Learning (2nd edition)" book code repository and info resource

python_for_bio

Teaching material for Python for Biomodellers Course

pytorch-gan

PyTorch implementations of Generative Adversarial Networks.

pytorch-sentiment-analysis

Tutorials on getting started with PyTorch and TorchText for sentiment analysis.

pytorch-tutorial

Build your neural network easy and fast

qtools

qtools is a Python interface library (Qpyl) and a set of useful command line tools for working with the Q molecular dynamics simulation package.