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openmm-forcefields

CHARMM and AMBER forcefields for OpenMM

opensol

opsin

Open Parser for Systematic IUPAC Nomenclature. Chemical name to structure conversion

parallel-plants

Parallel Molecular Docking using PLANTS software

parmed

Parameter/topology editor and molecular simulator

parsefep

A development branch of the VMD plugin to analyze NAMD's free energy calculations

passerrank

pbxplore

A suite of tools to explore protein structures with Protein Blocks :snake:

pdb2pdbqt

Converting PDB file to pdbqt file for autodock

pdb2pqr

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

pdb2pqr_flask

Trying to bring the PDB2PQR web server into the 21st century

pdbfixer

PDBFixer fixes problems in PDB files

pdbqt-to-mol2

convert autodock ligand pdbqt to mol2 with original mol2 as reference

pk-sim

PK-Sim® is a comprehensive software tool for whole-body physiologically based pharmacokinetic modeling

pkasolver

toolkit for prediction pKa values of small molecules via graph convolutional networks

pkasolver-data

Data repository for pkasolver

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

plot_utils

utilities for plotting with matplotlib

plugin-esp

Calculate ElectroStatic Potential Maps using APBS

pmx

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

pocketsimilarityapproach

This repository have pocket matching automation scripts

propka-3.1

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

protac-model

Integrative modeling of PROTAC-mediated ternary complex

protein_feature_analysis

ProteinFeatureAnalyzer extracts, analyzes and visualizes features from protein structures.

protocaller

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

psi4

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

psiresp

RESP with inter- and intra-molecular constraints in Psi4.

public-models

This repository contains the code that is relevant to the training of the Jaqpot public models. These are 22 ML/AI models, trained on the data of the Therapeutics Data Commons ADME-Tox (ADMET) Benchmark group and are suitable for small molecule drug discovery.

pyautofep

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

pyautofep_gromacs_fep