56 skills found · Page 1 of 2
prody / ProDyA Python Package for Protein Dynamics Analysis
AspirinCode / Awesome AI4MolConformation MDList of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning
ingcoder / UnomdPython package to run molecular dynamics simulation of a protein-ligand complex in a single line of code.
WaymentSteeleLab / Dyna 1Model for predicting micro-millisecond motions from protein sequence and/or structure
John-Jumper / Upside MDCoarse-grained molecular dynamics for protein physics
Pranavkhade / PACKMANPython package built around protein structure and dynamics. OpenBabel-inspired objects.
TheVisualHub / RoyalMD👑 A lightweight molecular dynamics pipeline for running protein simulations on portable hardware
Jhsmit / PyHDXDerive ΔG for single residues from HDX-MS data
philipwfowler / Simple Membrane Protein AnalysisThis is a short tutorial showing how to use both VMD and MDAnalysis to analyse a molecular dynamics simulation of a membrane protein.
szymonzaczek / MDMSMDMS: Molecular Dynamics Made Simple; Python program facilitating performing Molecular Dynamics simulations of proteins
xuhuihuang / GME TutorialsTutorials for non-Markovian dynamic models (qMSM and IGME) to study protein dynamics.
sosnicklab / Upside MdCoarse-grained molecular dynamics for protein physics. NOTE: this has been superseded by Upside 2: https://github.com/sosnicklab/upside2-md
Bhattacharya-Lab / PolyFoldAn interactive visual simulator for distance-based protein folding
brueckna2020 / MDFitAutomated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics
djmaity / Md DavisMD DaVis: A python package to analyze molecular dynamics trajectories of proteins
alirezaomidi / AFM IDROfficial repo for paper "AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions"
adityasengar / GLDPOfficial Python implementation for the paper accepted at ICLR 2026 'Beyond Ensembles: Simulating All-Atom Protein Dynamics in a Learned Latent Space'.
Degiacomi-Lab / JabberDockprotein docking using a density-based descriptor for atoms charge and dynamics
Gervasiolab / Gervasio Protein DynamicsA repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery
idrblab / MoDAFoldan innovative strategy for missense mutant protein structures prediction based on AlphaFold2 and Molecular Dynamics Simulation
