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molecular-modeling

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MolecularNodes

BradyAJohnston /MolecularNodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

blender proteins structural-biology pdb protein-data-bank protein-structure visualisation molecule molecular-dynamics molecular-graphics protein biochemistry molecular blender-addon molecular-modeling sciart protein-visualization geometry-nodes

UpdatedNov 6, 2025
Python

deepmodeling /Uni-Mol

Official Repository for the Uni-Mol Series Methods

deep-learning molecular-modeling pre-trained-model pretraining

UpdatedMay 29, 2025
Python

3dmol /3Dmol.js

WebGL accelerated JavaScript molecular graphics library

computational-biology molecular-graphics computational-chemistry molecular-modeling

UpdatedOct 5, 2025
Jupyter Notebook

gnina /gnina

A deep learning framework for molecular docking

cheminformatics computational-chemistry drug-discovery convolutional-neural-networks molecular-modeling

UpdatedNov 3, 2025
C++

isayev /ReLeaSE

Deep Reinforcement Learning for de-novo Drug Design

reinforcement-learning cheminformatics drug-discovery deeplearning qsar molecular-modeling

UpdatedDec 8, 2021
Jupyter Notebook

markovmodel /PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂

python markov-model hmm time-series analysis molecular-dynamics bayesian-methods tica hidden-markov-model markov-state-model umbrella-sampling mbar kinetic-modeling molecular-modeling

UpdatedSep 11, 2023
Python

forlilab /Meeko

Interface for AutoDock, molecule parameterization

chemistry drug-discovery drug-design molecular-modeling drug-target-interactions

UpdatedNov 1, 2025
Python

stk

lukasturcani /stk

A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

chemistry cheminformatics molecular-structures computational-chemistry reactions materials-science molecular-evolution computational-science molecular-modeling materials-screening materials-discoveries materials-design

UpdatedNov 5, 2025
Python

ClapeyronThermo /Clapeyron.jl

Clapeyron provides a framework for the development and use of fluid-thermodynamic models, including SAFT, cubic, activity, multi-parameter, and COSMO-SAC.

julia thermodynamics equation-of-state solvers saft molecular-modeling unifac phase-equilibrium cosmo-sac phase-equilibria

UpdatedNov 6, 2025
Julia

Acellera /moleculekit

MoleculeKit: Your favorite molecule manipulation kit

machine-learning proteins molecule molecular-simulation drug-discovery molecular-modeling

UpdatedOct 21, 2025
Python

nablaDFT

AIRI-Institute /nablaDFT

nablaDFT: Large-Scale Conformational Energy and Hamiltonian Prediction benchmark and dataset

benchmark machine-learning dft density-functional-theory dataset quantum-chemistry molecular-modeling

UpdatedMar 20, 2025
Python

Transformer-M

lsj2408 /Transformer-M

[ICLR 2023] One Transformer Can Understand Both 2D & 3D Molecular Data (official implementation)

molecule transformer molecular-modeling graph-neural-network graph-transformer general-purpose-molecular-model

UpdatedMar 31, 2023
Python

mojaie /MolecularGraph.jl

Graph-based molecule modeling toolkit for cheminformatics

chemistry graph cheminformatics toolkit julia molecule julia-language mcs molecular-modeling

UpdatedOct 19, 2025
Julia

Fermi.jl

FermiQC /Fermi.jl

Fermi quantum chemistry program

chemistry julia physics quantum-chemistry mp2 hartree-fock molecular-modeling coupled-cluster

UpdatedJun 26, 2025
Julia

TinkerTools /tinker

Tinker: Software Tools for Molecular Design

molecular-dynamics force-fields molecular-mechanics molecular-modeling biomolecular-simulation

UpdatedOct 28, 2025
Fortran

openpathsampling /openpathsampling

An open source Python framework for transition interface and path sampling calculations.

monte-carlo molecular-dynamics molecular-dynamics-simulation molecular-modeling biomolecular-simulation path-sampling

UpdatedJun 6, 2025
Python

aiqm /aimnet

Atoms In Molecules Neural Network Potential

deep-learning neural-network chemistry quantum-mechanics molecular-dynamics molecular-simulation quantum-chemistry molecular-modeling

UpdatedNov 21, 2019
Python

isayev /ANI1_dataset

A data set of 20 million calculated off-equilibrium conformations for organic molecules

machine-learning chemistry cheminformatics molecular-structures opendata molecular-modeling

UpdatedAug 8, 2022
Python

openmm /NNPOps

High-performance operations for neural network potentials

machine-learning gpu cuda molecular-dynamics molecular-modeling

UpdatedFeb 28, 2025
C++

swsoyee /r3dmol

🧬 An R package for visualizing molecular data in 3D

visualization r protein-structure computational-biology molecular-graphics protein computational-chemistry htmlwidgets hacktoberfest 3d molecular-modeling

UpdatedOct 25, 2023
JavaScript

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