task-trajectory-analysis

Solvation Structure and Thermodynamic Mapping

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

Biomolecular simulation trajectory/data analysis.

🚂 Python API for Emma's Markov Model Algorithms 🚂

Detect and characterize binding pockets from molecular simulations.

PyRod - Tracing water molecules in molecular dynamics simulations

MD pharmacophores and virtual screening

🏗️ Statistical models for biomolecular dynamics 🏗️

A pocket volume analyzer for use in protein modeling.

MD trajectory analysis using protein-ligand Interaction Fingerprints

Powerful, efficient particle trajectory analysis in scientific Python.

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

Contact map analysis for biomolecules; based on MDTraj

Python interface of cpptraj

Cryptic binding pocket discovery from conformational ensembles. Open-source, reproducible, size-robust benchmarks against fpocket, PocketMiner and CryptoBench.

Development version of plumed 2

HTMD: Programming Environment for Molecular Discovery

A Python Package for Protein Dynamics Analysis

Fast and All atom Protein-Ligand Interaction Profiler

Dynamic pharmacophore modeling of molecular interactions