An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: molecular-modeling

JayLau123/Machine-learning-for-Materials

CGCNN for inorganic solid materials

Language: Jupyter Notebook - Size: 12.6 MB - Last synced at: about 21 hours ago - Pushed at: about 23 hours ago - Stars: 6 - Forks: 0

uibcdf/molsysmt

Open source library to work with molecular systems

Language: Python - Size: 379 MB - Last synced at: about 22 hours ago - Pushed at: about 23 hours ago - Stars: 13 - Forks: 3

mitkeng/peas

A user-friendly application for precise conformation sampling

Language: Jupyter Notebook - Size: 1.79 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 2 - Forks: 0

3dmol/3Dmol.js

WebGL accelerated JavaScript molecular graphics library

Language: Jupyter Notebook - Size: 1.01 GB - Last synced at: 1 day ago - Pushed at: about 1 month ago - Stars: 895 - Forks: 210

denoptim-project/AutoCompChem

Tools for automated computational chemistry

Language: Java - Size: 87.7 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 4 - Forks: 0

Acellera/moleculekit

MoleculeKit: Your favorite molecule manipulation kit

Language: Python - Size: 115 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 226 - Forks: 41

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.

Language: Julia - Size: 81.5 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 254 - Forks: 64

stevnBasbak/CDOCKER-a-concensus-docking-tool

A bash based concencus molecular docking tool, combining different docking tools with advanced data analysis to provide insight in molecule - receptor docking.

Language: Python - Size: 7.82 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

openforcefield/yammbs

Internal tool for benchmarking force fields

Language: Jupyter Notebook - Size: 19.2 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 4 - Forks: 2

Degiacomi-Lab/molearn

protein conformational spaces meet machine learning

Language: Python - Size: 226 MB - Last synced at: 2 days ago - Pushed at: 3 months ago - Stars: 47 - Forks: 15

gnina/gnina

A deep learning framework for molecular docking

Language: C++ - Size: 241 MB - Last synced at: 1 day ago - Pushed at: 26 days ago - Stars: 766 - Forks: 164

TinkerTools/tinker

Tinker: Software Tools for Molecular Design

Language: Fortran - Size: 132 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 144 - Forks: 72

JureCerar/flat

Collection of PyMOL scripts and utilities

Language: Python - Size: 910 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

DoNOF/DoNOFsw

Donostia Natural Orbital Functional Software

Language: BASIC - Size: 9.81 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 20 - Forks: 6

GANGTONGH/Discrete-Molecular-Dynamics-Data-Analysis-Toolkit

This GitHub repository contains utility programs for the analysis of simulation data generated by Discrete Molecular Dynamics.

Language: Python - Size: 4.92 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 3 - Forks: 0

ravilokhande1396/MOLECULAR-SIMULATION-DYNAMICS

CHE 622 PROJECT

Language: Python - Size: 812 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

Open-Quantum-Platform/openqp

The main repository of Open Quantum Platform (OpenQP) maintained by Choi Group at KNU.

Language: Fortran - Size: 41 MB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 38 - Forks: 13

prescient-design/jamun

Bridging Smoothed Molecular Dynamics and Score-Based Learning for Conformational Ensembles

Language: Python - Size: 166 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 10 - Forks: 1

h-brough/TUNA

A user-friendly quantum chemistry program for diatomics.

Language: Python - Size: 10.3 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 1 - Forks: 0

mojaie/MolecularGraph.jl

Graph-based molecule modeling toolkit for cheminformatics

Language: Julia - Size: 5.64 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 212 - Forks: 28

forlilab/Meeko

Interface for AutoDock, molecule parameterization

Language: Python - Size: 7.83 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 273 - Forks: 59

GMPavanLab/dynsight

A framework for the analysis of the dynamics of particle trajectories

Language: Python - Size: 102 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 2 - Forks: 6

patrickallanfaustino/tutorials-md

Tutorials molecular dynamics.

Language: Makefile - Size: 6.2 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

BradyAJohnston/MolecularNodes

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

Language: Python - Size: 923 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 1,066 - Forks: 98

pedro-tulio/amdenm

Setup, run and analyse Adaptive MDeNM simulations on CHARMM

Language: Shell - Size: 121 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

pedro-tulio/pyadmd

Setup and run aMDeNM simulations with Python

Language: Python - Size: 3.72 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

yboulaamane/awesome-drug-discovery

A meticulously curated resource list focused on computational methods for drug discovery.

Size: 563 KB - Last synced at: 15 days ago - Pushed at: 16 days ago - Stars: 42 - Forks: 11

Augus1999/bayesian-flow-network-for-chemistry

ChemBFN: Bayesian Flow Network Framework for Chemistry Tasks. Developed in Hiroshima University.

Language: Python - Size: 688 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 25 - Forks: 4

mitkeng/SEER

Gas phase molecular charge state predictor

Language: Jupyter Notebook - Size: 1.04 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 2 - Forks: 0

uibcdf/enmmt

Open source library to work with elastic network models

Language: Jupyter Notebook - Size: 7.45 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 4 - Forks: 3

zotko/xyz2graph

Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.

Language: Python - Size: 7.47 MB - Last synced at: 1 day ago - Pushed at: 19 days ago - Stars: 86 - Forks: 23

yesint/molar

Repository for molar crate and its dependencies

Language: Rust - Size: 102 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 34 - Forks: 2

HySonLab/EquiHGNN

Rotationally Equivariant Hypergraph Neural Networks (EquiHGNN)

Language: Python - Size: 17.8 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 11 - Forks: 2

Edinburgh-Chemistry-Teaching/MD_ResearchTechniques

Materials for the "Introduction to Computational Chemistry Techniques" course at the University of Edinburgh

Language: HTML - Size: 277 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 2 - Forks: 3

TinkerTools/tinker-gpu

Tinker-GPU: Next Generation of Tinker with GPU Support

Language: C++ - Size: 43.2 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 51 - Forks: 29

NoahHenrikKleinschmidt/buildamol

A fragment-based molecular assembly toolkit

Language: Python - Size: 183 MB - Last synced at: 20 days ago - Pushed at: about 1 month ago - Stars: 38 - Forks: 1

HartreeFoca/BasisSets.jl

Package to parse Basis Sets from Basis Set Exchange API

Language: Mathematica - Size: 12.5 MB - Last synced at: 17 days ago - Pushed at: about 1 month ago - Stars: 8 - Forks: 1

Institute-for-Future-Intelligence/aims

AIMS: Artificial Intelligence for Molecular Sciences

Language: TypeScript - Size: 223 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 2

quimiquilla/ritonavir_milling

Language: Python - Size: 131 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

kmcos/kmcos

Kinetic Monte Carlo of Systems (KMCOS): lattice based kinetic Monte Carlo with a python front-end and Fortran back-end.

Language: Fortran - Size: 29.6 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 23 - Forks: 18

sdgbdhsgd/molecular

Explore molecular structures with the Molecular web app. Animate and visualize with React and TypeScript for an interactive experience. 🌐✨ #GitHub

Language: TypeScript - Size: 375 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

bowman-lab/enspara

Modeling molecular ensembles with scalable data structures and parallel computing

Language: Python - Size: 9.29 MB - Last synced at: 5 days ago - Pushed at: about 1 month ago - Stars: 36 - Forks: 17

m3g/ComplexMixtures.jl

Package to perform minimum-distance distribution analyses of complex solute-solvent interactions

Language: Julia - Size: 60.9 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 20 - Forks: 3

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.

Language: Python - Size: 45 MB - Last synced at: 3 days ago - Pushed at: about 2 months ago - Stars: 267 - Forks: 51

markovmodel/PyEMMA πŸ“¦

πŸš‚ Python API for Emma's Markov Model Algorithms πŸš‚

Language: Python - Size: 10.3 MB - Last synced at: 23 days ago - Pushed at: almost 2 years ago - Stars: 327 - Forks: 124

dgront/BioShell

Rust package for structure biology, bioinformatics and molecular modeling

Language: Rust - Size: 6.86 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 7 - Forks: 1

Vendogor/DataCon2025_SymmetryGroup Fork of kirill1604/The-symmetry-group

ITMO DataCon 2025: Hacking Drug Discovery/Design with Computational Pharmacology

Language: Jupyter Notebook - Size: 16.4 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

AkshaySyal/Predictive-Modeling-with-BELKA-Chemical-Libraries

A machine learning–driven project that predicts small molecule–protein binding using the BELKA dataset, aiming to accelerate drug discovery by modeling interactions across vast chemical space.

Language: Jupyter Notebook - Size: 2.21 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

themagiulio/bbtools

A collection of scripts and programs for biomolecules modeling and simulations.

Language: Python - Size: 25.4 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

JulianPalmisano/VitalSim3D

Open-source Python app for real-time, interactive 3D visualization of a neural cell's response to stimuli.

Language: Python - Size: 121 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

isayev/ANI1_dataset

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

Language: Python - Size: 2.62 MB - Last synced at: 18 days ago - Pushed at: about 3 years ago - Stars: 98 - Forks: 17

pyMBE-dev/pyMBE

pyMBE provides tools to facilitate building up molecules with complex architectures in the Molecular Dynamics software ESPResSo. For an up-to-date API documention please check our website:

Language: Python - Size: 5.54 MB - Last synced at: 7 days ago - Pushed at: 2 months ago - Stars: 12 - Forks: 12

mlund/pdb2xyz

Convert PDB files to coarse grained XYZ files

Language: Python - Size: 105 KB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

Abdelazim-Abdelgawwad/easyPARM

easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems and to enable charge restraints on specific atoms.

Language: Python - Size: 9.51 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 19 - Forks: 1

alibaba/graph-gpt

Generative Pre-trained Graph Eulerian Transformer [ICML2025]

Language: Python - Size: 4.81 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 84 - Forks: 6

IsabelThompson97/VersionControlled

Language: Python - Size: 32.8 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

FermiQC/Fermi.jl

Fermi quantum chemistry program

Language: Julia - Size: 43.4 MB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 153 - Forks: 26

openpathsampling/openpathsampling

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

Language: Python - Size: 268 MB - Last synced at: 1 day ago - Pushed at: 3 months ago - Stars: 112 - Forks: 49

smparker/molecular-blender

blend molecules!

Language: Python - Size: 6.49 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 37 - Forks: 7

yesint/pteros

Modern and fast molecular analysis and modeling library for C++ and Python

Language: C++ - Size: 18.1 MB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 35 - Forks: 8

sourceduty/Chemtronics

Research and develop novel functional materials with unique electronic properties for advanced applications.

Size: 6.84 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

BlueBrain/MultiscaleRun πŸ“¦

Python package to run brain cells simulation at different scales

Language: Jupyter Notebook - Size: 95.9 MB - Last synced at: 2 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 1

chrisjonesBSU/mosdef-containers

Docker containers for MoSDeF

Size: 95.7 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

theochem/B3clf

Predictors for Blood-Brain Barrier Permeability with resampling strategies based on B3DB database.

Language: Python - Size: 218 MB - Last synced at: 3 months ago - Pushed at: 8 months ago - Stars: 10 - Forks: 4

fazekaszs/loco_hd

The LoCoHD metric for protein-protein structure comparison

Language: Python - Size: 4.53 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 14 - Forks: 2

rlaplaza/libarvo

Library to compute molecular surfaces and volumes.

Language: Fortran - Size: 94.7 KB - Last synced at: 10 days ago - Pushed at: almost 3 years ago - Stars: 7 - Forks: 0

deepmodeling/Uni-Mol

Official Repository for the Uni-Mol Series Methods

Language: Python - Size: 22.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 866 - Forks: 142

OJB-Quantum/BlenderPy-Scripts

For performing data-driven 3D modeling & rendering. Useful Python scripts that can be copied into Blender under its scripting tab.

Language: Python - Size: 2.69 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 8 - Forks: 0

aqlaboratory/pnerf

Language: Python - Size: 60.5 KB - Last synced at: 8 days ago - Pushed at: about 6 years ago - Stars: 36 - Forks: 5

simahashemi/Block-Copolymer-Escape-Dynamics-Simulation

Simulation of block copolymer escape dynamics using a bead-spring model with Monte Carlo and forward-flux sampling. Includes free-energy profiling via umbrella sampling and escape rate estimation from micelle cores.

Language: Python - Size: 562 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

JelfsMaterialsGroup/stko

A collection of molecular optimisers and property calculators for use with stk.

Language: Python - Size: 36.9 MB - Last synced at: 2 months ago - Pushed at: 4 months ago - Stars: 24 - Forks: 9

MengjieChan/MolecBioNet

Towards Interpretable Drug-Drug Interaction Prediction: A Graph-Based Approach with Molecular and Network-Level Explanations

Language: Python - Size: 63.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

denoptim-project/DENOPTIM

DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind.

Language: Java - Size: 165 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 37 - Forks: 10

Killercavin/protein-binding

A protein binding and molecular screening platform

Language: TypeScript - Size: 1.22 MB - Last synced at: 27 days ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

motagfr/molecular-machine-learning-kaggle

Machine learning for molecular property prediction (Kaggle). Includes RDKit-powered visualization and analysis of molecular structures from SMILES.

Language: Jupyter Notebook - Size: 3.67 MB - Last synced at: 8 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

yesint/hccp

Hierarchical Clustering of Correlation Patterns (HCCP) algorithm

Language: Fortran - Size: 381 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

andrewtarzia/PoreMapper

cavity shape and size mapping by growing a guest inside a host

Language: Python - Size: 505 KB - Last synced at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 1

ramirezlab/ramirezlab.github.io

The Website of the RamirΓ©z Lab

Language: HTML - Size: 349 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 1

MrBlankCoding/Molecule-3d-Visualisation

A project for interactive 3D simulations of molecules, built with Three.js.

Language: JavaScript - Size: 85 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 1

lsj2408/Transformer-M

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

Language: Python - Size: 5.45 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 209 - Forks: 26

DevSlem/Mol-AIR

Molecular Reinforcement Learning with Adaptive Intrinsic Reward for Goal-directed Molecular Generation.

Language: Python - Size: 11.7 MB - Last synced at: 4 months ago - Pushed at: 6 months ago - Stars: 15 - Forks: 3

isayev/ReLeaSE

Deep Reinforcement Learning for de-novo Drug Design

Language: Jupyter Notebook - Size: 439 MB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 359 - Forks: 139

lukasturcani/mol-draw

A lightweight, 3D molecular viewer for JavaScript and PureScript applications.

Language: PureScript - Size: 1.7 MB - Last synced at: 28 days ago - Pushed at: over 2 years ago - Stars: 21 - Forks: 3

ibmm-unibe-ch/glycosylator

A Python framework for the rapid modeling of glycans

Language: Python - Size: 312 MB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 15 - Forks: 0

dogeplusplus/qm9-gnn

Language: Python - Size: 164 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

Pengfei-Liu-SYSU/NPS-FACL

The NPS-FACL project develops a LLM-based model to classify novel psychoactive substances, enhancing forensic toxicology through fragment-aware tokenization and explainable uncertainty quantification.

Language: Jupyter Notebook - Size: 1.67 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

KrumkachevaLab/EPR-BindingSite

Identification of Protein-Ligand Binding Sites using dipolar EPR data

Language: Jupyter Notebook - Size: 5.56 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

AIRI-Institute/nablaDFT

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

Language: Python - Size: 67.1 MB - Last synced at: 5 months ago - Pushed at: 6 months ago - Stars: 202 - Forks: 22

moritzobenauer/ProjectRaccoon

Automated construction of atomistic and coarse-grained models in the PDB format for polymer peptide conjugates.

Language: Jupyter Notebook - Size: 8.37 MB - Last synced at: 2 days ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 1

GMPavanLab/Swarm-CG

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

Language: Python - Size: 32.1 MB - Last synced at: 17 days ago - Pushed at: about 1 year ago - Stars: 45 - Forks: 12

DrugBud-Suite/CADD_Vault

Language: HTML - Size: 17.7 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 43 - Forks: 5

openmm/NNPOps

High-performance operations for neural network potentials

Language: C++ - Size: 232 KB - Last synced at: 3 months ago - Pushed at: 6 months ago - Stars: 93 - Forks: 19

ISDementyev/pmUE

pmUE (Protein Modelling Unreal Engine) - a repo for constructing a molecule visualizer plugin in Unreal

Language: C++ - Size: 37.2 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 6 - Forks: 3

HongxinXiang/ImageMol

ImageMol is a molecular image-based pre-training deep learning framework for computational drug discovery.

Language: Python - Size: 151 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 51 - Forks: 26

andthum/lintf2_ether_ana_postproc

Analysis postprocessing utilities for my molecular dynamics simulations of LiTFSI-Ether mixtures

Language: Python - Size: 1.22 MB - Last synced at: 1 day ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0

andthum/transfer_Li

Transfer Li ions from cathode to anode in MD simulations

Language: Shell - Size: 201 KB - Last synced at: 2 days ago - Pushed at: 20 days ago - Stars: 2 - Forks: 0

andthum/mdtools

Scripts to prepare and analyze molecular dynamics simulations

Language: Python - Size: 12.7 MB - Last synced at: 2 days ago - Pushed at: 12 days ago - Stars: 9 - Forks: 2

mayankmittal29/MolSim-Modelling-Chemistry-and-Analysis

This computational chemistry project delves into quantum mechanical analyses of various molecular systems using state-of-the-art computational methods. Through the application of Hartree-Fock (HF) theory with the STO-3G basis set in Gaussian software, we explore reaction energetics, molecular conformations, and spectroscopic properties

Language: DIGITAL Command Language - Size: 6.16 MB - Last synced at: 2 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

steviecurran/CO-column

Claculates the column density of interstellar molecular gas

Language: PHP - Size: 198 KB - Last synced at: 6 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

raulorteg/ImplicitGeom

Obtaining 'some estimate' of the 3D geometry of a molecule from its adjacency matrix without forces or energies.

Language: Python - Size: 124 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

Related Keywords
molecular-modeling 202 molecular-dynamics 55 computational-chemistry 41 chemistry 29 molecular-simulation 28 cheminformatics 27 molecular-dynamics-simulation 26 drug-discovery 20 bioinformatics 20 machine-learning 19 quantum-chemistry 16 python 15 protein-structure 15 drug-design 12 computational-biology 11 molecular-structures 8 molecular-mechanics 7 gromacs 7 molecule 7 molecular-docking 7 deep-learning 7 molecules 7 materials-science 7 proteins 6 visualization 6 science 6 protein 6 structural-biology 5 gaussian 5 graph-neural-networks 5 biochemistry 4 pdb 4 force-fields 4 pytorch 4 computational-physics 4 blender 4 ai 4 simulation 4 density-functional-theory 4 optimization 4 artificial-intelligence 4 qsar 4 transformer 4 molecular-graphics 4 virtual-screening 4 julia 4 scientific-computing 4 docking 4 computational-science 4 molsysmt 3 trajectory-analysis 3 molecular-biology 3 pdb-files 3 diffusion-models 3 pymol 3 molecule-visualization 3 coarse-graining 3 python-scripts 3 compchem 3 namd 3 physics 3 mdanalysis 3 elastic-network-models 3 pymol-plugin 3 geometric-deep-learning 3 chemoinformatics 3 monte-carlo-simulation 3 amber 3 blender-addon 3 molecular-design 3 biomolecular-simulation 3 graph 3 cuda 3 mccs 3 molecular 3 gpt 2 python-3 2 data-visualization 2 web-application 2 high-throughput 2 normal-modes 2 molecular-docking-scripts 2 monte-carlo 2 forcefield 2 structure-activity-relationships 2 generative-adversarial-network 2 umbrella-sampling 2 rosetta 2 neuroscience 2 molecular-evolution 2 lammps 2 markov-state-model 2 kinetic-modeling 2 biophysics 2 tensorflow-gpu 2 protein-ligand 2 molecular-modelling 2 gnn-model 2 r 2 quantum-mechanics 2