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paprika-kcl

A playground for binding free energy calculations with pAPRika

paprika-tutorial

pdb-redo

PDB_REDO

pdb-topology-viewer

PDB Topology Viewer

pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

pdbe-molstar

Molstar PDBe implementation

pdbfinder

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

pdbfixer

PDBFixer fixes problems in PDB files

pdbmutator

PDBmutator is a GUI enabled script to batch run swapna or swapaa commands in UCSF Chimera software on a PDB file. It creates all possible structural mutants for a given sequence, OR alternatively it creates variants defined by a CLUSTAL file protein alignment.

pdbtools

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

perses

Experiments with expanded ensembles to explore chemical space

pimento

Protein methyltransferases

plantgl

An open-source graphic toolkit for the creation, simulation and analysis of 3D virtual plants.

plasmidlibrarytools

PlasmidLibraryTools

plateo

🤖 Python biolab automation library: parsers, reports generators, picklists simulators, and more

plbenchmarks

Protein-Ligand Benchmark Dataset for Free Energy Calculations

pmda

Parallel algorithms for MDAnalysis

printable-3d-parts

Useful parts that can be 3D printed.

prkg2_analysis

In silico analysis of the cGMP-dependent protein kinase 2 (PRKG2 encoded)

prolif

Protein-Ligand Interaction Fingerprints

protein-ligand-benchmarks

Protein-ligand benchmarks for free energy calculations

protoms

ProtoMS is a program to setup, run and analyse Monte Carlo simulations of organic and biomolecular systems.

protons

OpenMM testbed for constant-pH methodologies.

protvista-pdb

PDB ProtVista Viewer

pybel

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

pyeasyga

A simple and easy-to-use implementation of a Genetic Algorithm library in Python

pykeen

🤖 A Python library for learning and evaluating knowledge graph embeddings

pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

pymol-script-repo

Collected scripts for Pymol

qcelemental

Periodic table, physical constants, and molecule parsing for quantum chemistry.