rdk/p2rank

P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

Language: Groovy - Size: 676 MB - Last synced at: about 9 hours ago - Pushed at: 29 days ago - Stars: 343 - Forks: 49

BioPandas/biopandas

Working with molecular structures in pandas DataFrames

Language: Python - Size: 22.3 MB - Last synced at: 1 day ago - Pushed at: about 1 year ago - Stars: 737 - Forks: 118

sirius-ms/sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Language: Java - Size: 178 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 115 - Forks: 30

project-gemmi/gemmi

macromolecular crystallography library and utilities

Language: C++ - Size: 9.93 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 283 - Forks: 50

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: 6 days ago - Pushed at: 7 days ago - Stars: 3 - Forks: 0

lightdock/lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Language: Python - Size: 93.4 MB - Last synced at: 1 day ago - Pushed at: 2 months ago - Stars: 353 - Forks: 47

nglviewer/ngl

WebGL protein viewer

Language: TypeScript - Size: 529 MB - Last synced at: 6 days ago - Pushed at: 5 months ago - Stars: 705 - Forks: 175

stfc/quantum-molecular-encodings

Data and codes used in Boy et al. (2025) - Quantum molecular structure encoding

Language: Jupyter Notebook - Size: 4.51 MB - Last synced at: about 12 hours ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0

lanl/Architector

The architector python package - for 3D metal complex design. C22085

Language: Python - Size: 14.2 MB - Last synced at: 16 days ago - Pushed at: about 1 month ago - Stars: 64 - Forks: 14

VHchavez/moly

Molecular Visualization powered by Plotly

Language: Python - Size: 1.59 MB - Last synced at: about 15 hours ago - Pushed at: about 3 years ago - Stars: 18 - Forks: 4

3dem/relion

Image-processing software for cryo-electron microscopy

Language: C++ - Size: 57.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 487 - Forks: 220

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: 2 days ago - Pushed at: about 2 months ago - Stars: 267 - Forks: 51

mims-harvard/ATOMICA

ATOMICA: Learning Universal Representations of Intermolecular Interactions

Language: Python - Size: 13.9 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 158 - Forks: 21

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: 17 days ago - Pushed at: about 3 years ago - Stars: 98 - Forks: 17

shehzaidi/pre-training-via-denoising

Official implementation of pre-training via denoising for TorchMD-NET

Language: Python - Size: 83.8 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 92 - Forks: 14

Jonas-Verhellen/Bayesian-Illumination

Bayesian Illumination is an accelerated generative model for optimization of small molecules.

Language: Jupyter Notebook - Size: 127 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 17 - Forks: 1

mariusmihasan/3DP-Jmol

3DP-JMol is a Jmol-based script that automatically generates 3D printable molecular models from structural data.

Size: 376 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - 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

shahabafshar/POSCAR3D

POSCAR3D is a 3D visualization tool for POSCAR files, offering realistic atom rendering based on van der Waals radii. Developed for researchers and students, it provides an interactive way to explore molecular structures with ease.

Language: Python - Size: 1.97 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

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

MooersLab/EasyPyMOL

Script to facilitate the making of horizontal scripts

Language: Python - Size: 646 KB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 19

Guillawme/chimerax-config

My configuration for UCSF ChimeraX

Size: 14.6 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

giotto-ai/molecule_bond_prediction

Predict scalar coupling in molecules

Language: Python - Size: 5.68 MB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 15 - Forks: 5

affjljoo3581/Samsung-AI-Challenge-for-Scientific-Discovery

🥇Samsung AI Challenge 2021 1등 솔루션입니다🥇

Language: Python - Size: 177 KB - Last synced at: 5 months ago - Pushed at: almost 4 years ago - Stars: 55 - Forks: 7

aksub99/molecular-vae

Pytorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"

Language: Jupyter Notebook - Size: 2.92 MB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 65 - Forks: 16

gky360/react-ngl

React wrapper for ngl

Language: TypeScript - Size: 5.03 MB - Last synced at: 3 days ago - Pushed at: over 2 years ago - Stars: 23 - Forks: 11

lukasturcani/stk-vis

A cross-platform application for visualization of molecular databases.

Language: PureScript - Size: 2.3 MB - Last synced at: 3 days ago - Pushed at: over 2 years ago - Stars: 33 - Forks: 4

fatipardo/PDBCleanV2

PDBClean helps create a curated ensemble of molecular structures

Language: Jupyter Notebook - Size: 4.05 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 6 - Forks: 0

zpengmei/SubFormer-Spec

SubFormer-Spec: Implementation of the graph Spectral token with SubFormer architecture

Language: Python - Size: 25.3 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 4 - Forks: 0

chembl/GLaDOS

Web Interface for ChEMBL @ EMBL-EBI

Language: JavaScript - Size: 43.5 MB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 46 - Forks: 6

insilichem/gaudiview

UCSF Chimera extension to explore and analyze GaudiMM & GOLD solutions

Language: Python - Size: 288 KB - Last synced at: 4 months ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 2

maxscheurer/pycontact

Analysis of non-covalent interactions in MD trajectories

Language: Python - Size: 53 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 51 - Forks: 11

marcocolangelo/MSSGAT Fork of leaves520/MSSGAT

Molecular substructure graph attention network for molecular property identification in drug discovery. This is the starting point for my thesis project and is the fork of a repository from the paper https://doi.org/10.1016/j.patcog.2022.108659

Language: Python - Size: 101 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

demianriccardi/p5-HackaMol

Object-Oriented Perl 5, Moose Library for Molecular Hacking

Language: Perl - Size: 2.39 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 12 - Forks: 6

skignatov/globus

Size: 13.9 MB - Last synced at: 12 months ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

Erastova-group/Biochar_MolecularModels

Molecular models of woody biochars at HTT 400C, 600C and 800C; and a collection of experimental property datasets for woody biochars

Language: Jupyter Notebook - Size: 28.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

FausticSun/DeepPL

Predicting Protein – Ligand Interaction by using Deep Learning Models

Language: Jupyter Notebook - Size: 7.77 MB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 11 - Forks: 1

stacs-srg/msp

MSP - Molecular Structure Predictor

Language: JavaScript - Size: 12.3 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 1

maxjr82/ws22-dashboard

Dashboard application to explore statistical features of the molecular datasets contained in the WS22 database.

Language: Python - Size: 18.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

Guillawme/chimerax-viz

Visualizations of macromolecular structures with UCSF ChimeraX

Language: Jupyter Notebook - Size: 310 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 1

mindleaving/genome-tools

Tools for exploration and analysis of biochemical data like genomics and proteins

Language: C# - Size: 905 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 2

stcmz/mccs-toolchain

This repository contains all in-house command-line tools served in the MCCS protocol.

Size: 15.6 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

JPatrickBrian/Redstone-Engineering

Open source molecular dynamics analysis tools for GROMACS

Language: Shell - Size: 94.4 MB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

opatiny/react-mol-structures

Responsive web app that returns possible structures isomers for an organic molecule.

Language: JavaScript - Size: 3.44 MB - Last synced at: 6 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

santuchal/ADMET_calculations

ADMET calculations from different research paper and a goal to make it memory efficent with ML implementations.

Size: 7.81 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

samuelrsilva/pdb2stl

Conversion of Protein Data Bank (PDB) structures for 3D printing

Language: C - Size: 99.6 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 6 - Forks: 4

TarekMebrouk/molecular_isomorphism

Retrieve the molecules from the ChEBI site, and parse them and extract the information important for the execution of the Nauty mckay algorithm.

Language: Python - Size: 103 KB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

intelsp/VELA

Origin of LIFE Research Project.

Size: 16.6 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

stardustcafe/molecularstats

Simple Package to calculate Molecular Weight of Compound with Brackets and Numbers.

Language: Python - Size: 42 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

naotohori/TIS2AA

Construct atomistic (AA) model from Three-Interaction-Site (TIS) coarse-grained model of RNA/DNA

Language: Python - Size: 3.29 MB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1

agiani99/KNIME_Screen

Collection scripts and workflows for data analysis on screening

Language: R - Size: 9.54 MB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 1

duboviy/pymolecule

:atom: Molecular viewer [Work in progress]

Language: Python - Size: 41 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 9 - Forks: 3

skignatov/moltran

Size: 19.7 MB - Last synced at: 12 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

srk/compchemtools

Utilities for manipulation/translation of input/output formats of quantum-mechanics based electronic structure codes

Language: Python - Size: 28.3 KB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 1

bbrighttaer/imagopy

A python wrapper for Imago OCR

Language: C++ - Size: 354 KB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 4

beebus/osra-iterate

Bash Script to iterate through .TIF Images in a folder and run the OSRA program to attempt to convert the TIF images into ChemDraw files (.CDXML).

Language: Shell - Size: 3.91 KB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

Yuchees/esf_explorer_templates

The templete for the web interactive ESF maps

Language: Python - Size: 3.63 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1

bammellab/bammellab.github.io

Bammellab web page contents

Size: 1.36 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

NU-CUCIS/SINet

A Transfer Learning Framework for Organic Solar Cell Prediction using Multi Input Single Output Neural Networks

Language: Jupyter Notebook - Size: 5.35 MB - Last synced at: over 2 years ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 3

MDSYN2019/PythonMDScripts

Folder containing the analysis code in C++/Python in MARTINI or SDK

Language: Python - Size: 127 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

kubawajs/PyRy3D-DisplayRestraints

Extension for creating visualizations of distance restraints in PyRy3D Chimera Extension

Language: Python - Size: 1.85 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

janeymunoz/bioinformatics

A set of tools for the acquisition and analysis of biological data.

Language: Python - Size: 29.3 KB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 0