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task-trajectory-analysis

Here are 22 public repositories matching this topic...

Scindices / markovmodel--PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂

lang-python status-archived entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-machine-learning method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit

Updated Sep 11, 2023
Python

Scindices / Amber-MD--cpptraj

Biomolecular simulation trajectory/data analysis.

status-active lang-cpp interface-cli task-file-io task-structure-analysis entity-protein entity-small-molecule interface-api status-published method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit scope-swissknife

Updated Jul 16, 2026
C++

Scindices / POVME--POVME3

A pocket volume analyzer for use in protein modeling.

lang-python status-archived interface-cli role-application domain-structural-biology entity-protein interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery task-pocket-detection method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

Updated Oct 2, 2022
Python

Scindices / wolberlab--pyrod

PyRod - Tracing water molecules in molecular dynamics simulations

status-active lang-python interface-cli role-application method-chemoinformatics entity-protein entity-small-molecule interface-api status-published scope-focused domain-drug-discovery method-physics domain-molecular-simulation task-trajectory-analysis entity-trajectory task-pharmacophore

Updated Oct 31, 2025
Python

Scindices / Valdes-Tresanco-MS--gmx_MMPBSA

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

status-active lang-python interface-cli role-application entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery method-physics entity-complex method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory task-free-energy

Updated Jul 27, 2026
Python

Scindices / HITS-MCM--MD-IFP

MD trajectory analysis using protein-ligand Interaction Fingerprints

status-active lang-python role-application method-chemoinformatics entity-protein entity-small-molecule interface-jupyter status-published scope-focused domain-drug-discovery entity-complex domain-molecular-simulation task-trajectory-analysis entity-trajectory ecosystem-mdanalysis task-interaction-analysis

Updated Sep 23, 2025
Jupyter Notebook

Scindices / KurtzmanLab--SSTMap

Solvation Structure and Thermodynamic Mapping

status-active lang-python lang-cpp interface-cli role-application entity-protein interface-api status-published scope-focused domain-drug-discovery method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory task-free-energy

Updated Dec 17, 2025
Python

Scindices / ci-lab-cz--pharmd

MD pharmacophores and virtual screening

lang-python status-archived interface-cli role-application method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery method-physics entity-complex domain-molecular-simulation task-trajectory-analysis entity-trajectory task-pharmacophore

Updated Dec 15, 2023
Python

Scindices / msmbuilder--msmbuilder

🏗️ Statistical models for biomolecular dynamics 🏗️

lang-python status-archived entity-protein interface-api status-published status-packaged-conda scope-focused method-machine-learning method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit

Updated Jan 26, 2021
Python

Scindices / durrantlab--POVME

Detect and characterize binding pockets from molecular simulations.

status-active lang-python interface-cli role-application entity-protein interface-api status-published scope-focused domain-drug-discovery task-pocket-detection method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

Updated Mar 17, 2026
Python

Scindices / MDAnalysis--mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

status-active lang-python task-file-io task-structure-analysis entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit ecosystem-mdanalysis scope-swissknife

Updated Jul 23, 2026
Python

Scindices / mdtraj--mdtraj

An open library for the analysis of molecular dynamics trajectories

status-active lang-python lang-c task-file-io task-structure-analysis entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit scope-swissknife

Updated Jul 29, 2026
Python

Scindices / glotzerlab--freud

Powerful, efficient particle trajectory analysis in scientific Python.

status-active role-library lang-python lang-cpp task-structure-analysis interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory entity-crystal domain-materials

Updated Jul 29, 2026
C++

Scindices / getcontacts--getcontacts

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

status-active lang-python interface-cli role-application domain-structural-biology entity-protein status-published scope-focused entity-complex domain-molecular-simulation task-trajectory-analysis entity-trajectory method-rule-based task-interaction-analysis

Updated Jun 28, 2026
Python

Scindices / wolberlab--dynophores

Dynamic pharmacophore modeling of molecular interactions

role-library lang-python status-archived method-chemoinformatics entity-protein entity-small-molecule interface-api interface-jupyter status-published status-packaged-conda domain-drug-discovery entity-complex method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory scope-swissknife task-pharmacophore task-interaction-analysis

Updated Apr 26, 2024
Promela

Scindices / BHM-Bob--fplip

Fast and All atom Protein-Ligand Interaction Profiler

status-active role-library lang-python interface-cli domain-structural-biology entity-protein entity-small-molecule interface-api status-packaged-pypi scope-focused domain-drug-discovery entity-complex task-trajectory-analysis entity-trajectory method-rule-based interface-gpu task-interaction-analysis

Updated Jul 27, 2026
Python

Scindices / Acellera--htmd

HTMD: Programming Environment for Molecular Discovery

status-active lang-python task-file-io entity-protein entity-small-molecule interface-api status-published status-packaged-conda method-physics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit scope-swissknife task-system-model

Updated Jul 29, 2026
Rich Text Format

Scindices / prody--ProDy

A Python Package for Protein Dynamics Analysis

status-active lang-python domain-structural-biology task-file-io task-structure-analysis entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit scope-swissknife

Updated Jul 22, 2026
Python

Scindices / plumed--plumed2

Development version of plumed 2

status-active lang-python lang-cpp interface-cli role-plugin entity-protein entity-small-molecule interface-api status-published status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory task-free-energy

Updated Jul 20, 2026
C++

Scindices / mooreneural--lacuna

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

status-active lang-python interface-cli role-application domain-structural-biology entity-protein interface-api scope-focused domain-drug-discovery task-pocket-detection method-machine-learning method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

Updated Jul 23, 2026
Python

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