molecular-structures

There are 6 repositories under molecular-structures topic.

BioPandas / biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Language:Python 678
nglviewer / ngl
WebGL protein viewer
webgl molecular-structures molecular-graphics web-application scientific-visualization javascript
Language:TypeScript 643
3dem / relion
Image-processing software for cryo-electron microscopy
microscopy cryo-em hpc cuda image-processing biomolecular-dynamics molecular-biology molecular-structures atomistic-models ctf high-performance-computing graphics-programming gui microscope optimization-algorithms maximum-likelihood likelihood relion regularization nvidia
Language:C++ 423
lightdock
lightdock / lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
protein protein-structure protein-protein-interaction protein-docking swarm-intelligence glowworm-swarm-optimization protein-dna-interactions peptides dna docking artificial-intelligence protein-design proteomics structural-biology structural-bioinformatics bioinformatics bioinformatics-tool chemistry molecular-biology molecular-structures
Language:Python 270
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 reactions computational-science computational-chemistry materials-science materials-design materials-discoveries materials-screening molecular-structures molecular-modeling molecular-evolution
Language:Python 234
p2rank
rdk / p2rank
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
bioinformatics machine-learning protein-structure pdb binding-sites proteins ligand protein-surface structural-bioinformatics protein-ligand-interactions java random-forest mmcif pymol groovy protein-ligand-docking molecular-structures drug-discovery virtual-screening p2rank
Language:Groovy 219
project-gemmi / gemmi
macromolecular crystallography library and utilities
ccp4 cif crystallography mmcif molecular-structures mtz pdb-files protein-structure structural-biology
Language:C++ 193
isayev / ANI1_dataset
A data set of 20 million calculated off-equilibrium conformations for organic molecules
machine-learning opendata chemistry cheminformatics molecular-structures molecular-modeling
Language:Python 92
shehzaidi / pre-training-via-denoising
Official implementation of pre-training via denoising for TorchMD-NET
deep-learning denoising denoising-autoencoders graph-neural-networks molecular-property-prediction molecular-structures pre-training pytorch score-matching
Language:Python 82
boecker-lab / 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)
denovo metabolomics mass-spectrometry java science cheminformatics bioinformatics molecular-structures molecular-formulas ms-spectra ms-data structure-elucidation fragmentation-trees sirius csi-fingerid fingerid isotope-pattern mass-spectra
Language:Java 75
aksub99 / molecular-vae
Pytorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"
cheminformatics pytorch materials-science materials-informatics python deep-learning variational-autoencoder molecular-structures machine-learning drug-discovery chemistry natural-language-processing jupyter-notebook
Language:Jupyter Notebook 58
affjljoo3581 / Samsung-AI-Challenge-for-Scientific-Discovery
🥇Samsung AI Challenge 2021 1등 솔루션입니다🥇
competition pytorch transformer molecular pubchem pubchemqc pytorch-lightning wandb deep-learning molecular-property-prediction dacon samsung molecular-structures deberta
Language:Python 49
maxscheurer / pycontact
Analysis of non-covalent interactions in MD trajectories
biophysics bioinformatics simulation biochemistry molecular-dynamics molecular-structures python qt5 analysis toolkit interactions dynamics chemistry computational-biology
Language:Python 46
chembl / GLaDOS
Web Interface for ChEMBL @ EMBL-EBI
chembl chemistry cheminformatics chemoinformatics webapp drug-targets drug-discovery molecular-structures
Language:JavaScript 40
lukasturcani / stk-vis
A cross-platform application for visualization of molecular databases.
molecules molecular-structures molecular-modeling chemistry cheminformatics visualization data-visualization database mongodb
Language:PureScript 32
lanl / Architector
The architector python package - for 3D metal complex design. C22085
actinides computational-chemistry d-block lanthanides molecular-simulation molecular-structures rare-earth-elements
Language:Python 31
gky360 / react-ngl
React wrapper for ngl
react ngl webgl molecular-structures web-application molecular-graphics scientific-visualization
Language:TypeScript 21
JelfsMaterialsGroup / stko
A collection of molecular optimisers and property calculators for use with stk.
cheminformatics cheminformatics-and-compchem chemistry computational-chemistry material-design molecular-modeling molecular-structures structure-optimization
Language:Python 19
lukasturcani / mol-draw
A lightweight, 3D molecular viewer for JavaScript and PureScript applications.
chemistry visualization molecular-modeling molecular-structures molecular-graphics
Language:PureScript 16
giotto-ai / molecule_bond_prediction
Predict scalar coupling in molecules
molecular-structures topological-data-analysis
Language:Python 14
MooersLab / EasyPyMOL
Script to facilitate the making of horizontal scripts
pymol pml horizontal-scripts molecular-graphics molecular-visuallization protein-structure molecular-artwork pymol-macro-language molecular-structures biomolecular-structures structural-bioinformatics ambient-occulsion black-and-white-cartoons coordinate-covalent-bonds rna-structure metal-coordination scripting tutorial-videos startup-aliases roundview
Language:Python 14
VHchavez / moly
Molecular Visualization powered by Plotly
jupyter plotly molecular-structures
Language:Python 14
demianriccardi / p5-HackaMol
Object-Oriented Perl 5, Moose Library for Molecular Hacking
molecular-structures modeling multiscale coarse-grained object-oriented
Language:Perl 12
FausticSun / DeepPL
Predicting Protein – Ligand Interaction by using Deep Learning Models
cs5242 deep-learning neural-network dataset molecular-structures
Language:Jupyter Notebook 11
duboviy / pymolecule
:atom: Molecular viewer [Work in progress]
molecule molecular-graphics molecules atoms-in-molecules atom molecular-structures pyglet pybel openbabel
Language:Python 9
samuelrsilva / pdb2stl
Conversion of Protein Data Bank (PDB) structures for 3D printing
pdb molecular-structures 3d-printing stl
Language:C 7
mindleaving / genome-tools
Tools for exploration and analysis of biochemical data like genomics and proteins
genomics genomic-data-analysis genomics-visualization molecular-dynamics molecular-structures molecule peptide molecular-simulation pdb pdb-files
Language:C# 5
fatipardo / PDBClean-0.0.2
PDBClean helps create a curated ensemble of molecular structures
cif-files cif-formats molecular-structures python
Language:Jupyter Notebook 4
Guillawme / chimerax-viz
Visualizations of macromolecular structures with UCSF ChimeraX
visualization pdb emdb macromolecules molecular-structures molecular-graphics chimerax ucsf-chimerax
Language:Jupyter Notebook 4
insilichem / gaudiview
UCSF Chimera extension to explore and analyze GaudiMM & GOLD solutions
visualization ucsf-chimera docking molecular-structures
Language:Python 4
agiani99 / KNIME_Screen
Collection scripts and workflows for data analysis on screening
knime workflow r molecular-structures
Language:R 3
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
biochar database molecular molecular-dynamics molecular-structures simulation
Language:Jupyter Notebook 3
janeymunoz / bioinformatics
A set of tools for the acquisition and analysis of biological data.
bioinformatics statistics molecular-structures string-manipulation
Language:Python 3
NU-CUCIS / SINet
A Transfer Learning Framework for Organic Solar Cell Prediction using Multi Input Single Output Neural Networks
deep-neural-networks transfer-learning chemistry machine-learning molecular-structures
Language:Jupyter Notebook 2
santuchal / ADMET_calculations
ADMET calculations from different research paper and a goal to make it memory efficent with ML implementations.
admet cheminformatics machine-learning molecular-structures predictive-analytics small-molecule molecular-des
2
stcmz / mccs-toolchain
This repository contains all in-house command-line tools served in the MCCS protocol.
molecular-structures molecule computational-chemistry
2