#
molecular-structures
Here are 46 public repositories matching this topic...
Working with molecular structures in pandas DataFrames
bioinformatics
pdb
molecular-structures
pandas-dataframe
protein-structure
molecule
computational-biology
drug-discovery
molecules
mol2
pdb-files
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Updated
Sep 24, 2021 - Python
Image-processing software for cryo-electron microscopy
gui
hpc
molecular-structures
cuda
image-processing
nvidia
high-performance-computing
graphics-programming
ctf
regularization
cryo-em
microscopy
likelihood
maximum-likelihood
optimization-algorithms
relion
molecular-biology
atomistic-models
biomolecular-dynamics
microscope
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Updated
Oct 5, 2021 - C++
andrewtarzia
commented
Jul 7, 2020
It would be a bit of fun to see if stk can handle building things like this: https://chemrxiv.org/articles/preprint/Isogonal_Weavings_on_the_Sphere_Knots_Links_Polycatenanes/12616268
macromolecular crystallography library and utilities
structural-biology
molecular-structures
protein-structure
crystallography
cif
ccp4
mmcif
pdb-files
mtz
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Updated
Oct 8, 2021 - C++
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
bioinformatics
chemistry
structural-biology
molecular-structures
protein-structure
artificial-intelligence
dna
protein
proteomics
docking
peptides
molecular-biology
protein-design
protein-protein-interaction
swarm-intelligence
structural-bioinformatics
protein-dna-interactions
bioinformatics-tool
glowworm-swarm-optimization
protein-docking
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Updated
Sep 30, 2021 - C
A data set of 20 million calculated off-equilibrium conformations for organic molecules
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Updated
Jun 5, 2018 - Python
New Web Interface for ChEMBL @ EMBL-EBI
chemistry
cheminformatics
molecular-structures
webapp
drug-discovery
chemoinformatics
chembl
drug-targets
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Updated
Jun 10, 2021 - JavaScript
A cross-platform application for visualization of molecular databases.
visualization
database
mongodb
chemistry
cheminformatics
molecular-structures
data-visualization
molecules
molecular-modeling
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Updated
Oct 6, 2021 - PureScript
Pytorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"
python
machine-learning
natural-language-processing
deep-learning
chemistry
cheminformatics
molecular-structures
jupyter-notebook
pytorch
drug-discovery
materials-science
materials-informatics
variational-autoencoder
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Updated
Mar 31, 2021 - Jupyter Notebook
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)
java
science
bioinformatics
cheminformatics
molecular-structures
sirius
metabolomics
mass-spectrometry
ms-data
denovo
molecular-formulas
ms-spectra
structure-elucidation
fragmentation-trees
csi-fingerid
fingerid
isotope-pattern
mass-spectra
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Updated
Oct 1, 2021 - Java
Analysis of non-covalent interactions in MD trajectories
python
bioinformatics
chemistry
analysis
simulation
toolkit
dynamics
molecular-structures
molecular-dynamics
computational-biology
qt5
biochemistry
interactions
biophysics
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Updated
Sep 1, 2020 - Python
React wrapper for ngl
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Updated
Jun 22, 2021 - TypeScript
Object-Oriented Perl 5, Moose Library for Molecular Hacking
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Updated
Apr 12, 2019 - Perl
Predict scalar coupling in molecules
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Updated
Mar 14, 2021 - Python
A lightweight, 3D molecular viewer for JavaScript and PureScript applications.
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Updated
Oct 6, 2021 - PureScript
Molecular viewer [Work in progress]
atom
molecular-structures
molecule
molecular-graphics
openbabel
molecules
pyglet
atoms-in-molecules
pybel
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Updated
Apr 26, 2020 - Python
Molecular Visualization powered by Plotly
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Updated
Aug 4, 2020 - Python
Predicting Protein – Ligand Interaction by using Deep Learning Models
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Updated
Nov 13, 2018 - Jupyter Notebook
Script to facilitate the making of horizontal scripts
molecular-structures
scripting
protein-structure
molecular-graphics
pymol
rna-structure
pml
structural-bioinformatics
tutorial-videos
horizontal-scripts
molecular-visuallization
molecular-artwork
pymol-macro-language
biomolecular-structures
ambient-occulsion
black-and-white-cartoons
coordinate-covalent-bonds
metal-coordination
startup-aliases
roundview
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Updated
Oct 4, 2018 - Python
Tools for exploration and analysis of biochemical data like genomics and proteins
genomics
pdb
molecular-structures
molecule
molecular-dynamics
molecular-simulation
genomic-data-analysis
genomics-visualization
pdb-files
peptide
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Updated
Oct 3, 2021 - C#
Conversion of Protein Data Bank (PDB) structures for 3D printing
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Updated
Jun 13, 2019 - C
A set of tools for the acquisition and analysis of biological data.
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Updated
May 15, 2018 - Python
UCSF Chimera extension to explore and analyze GaudiMM & GOLD solutions
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Updated
Apr 16, 2020 - Python
Visualizations of macromolecular structures with UCSF ChimeraX
visualization
pdb
molecular-structures
molecular-graphics
emdb
macromolecules
chimerax
ucsf-chimerax
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Updated
Oct 5, 2021 - Jupyter Notebook
Collection scripts and workflows for data analysis on screening
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Updated
Apr 17, 2020 - R
A python wrapper for Imago OCR
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Updated
Apr 21, 2019 - C++
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Updated
Feb 25, 2017 - Python
Folder containing the analysis code in C++/Python in MARTINI or SDK
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Updated
Sep 8, 2021 - Python
Open source molecular dynamics analysis tools for GROMACS
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Updated
Mar 13, 2020 - Shell
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.... and that maybe fine.... If you decide this is of no interest, that is very helpful too!
Details:
Structures Models of long transcripts (like Human gene TTN with over 30,000 residues) need residue numbering > 9999
Obviously, MMCIF format is the solution of the RCSB/PDBe
The UCSF Sali Lab Modbase group has adopted hybrid-36 format for these models. I left one of their models here