pymol

There are 4 repositories under pymol topic.

p2rank
rdk / p2rank
P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
binding-sites bioinformatics chimerax docking drug-discovery groovy java ligand machine-learning mmcif molecular-structures p2rank pdb protein-ligand-docking protein-ligand-interactions protein-structure proteins pymol structural-bioinformatics virtual-screening
Language:Groovy 356
cgohlke / pymol-open-source-wheels
Pymol-open-source wheels for Python on Windows.
pymol pymol-python python wheels windows
Language:Python 155
cbalbin-bio / pymol-color-alphafold
PyMOL extension to color AlphaFold structures by confidence (pLDDT).
alphafold alphafold2 bioinformatics computational-biology protein-structure structural-biology pymol pymol-plugin
Language:Python 114
MooersLab / pymolshortcuts
The repository pymolschortucts contains the a collection of shortcuts that are loaded on startup of PyMOL. These shortcuts enable websearches from within PyMOL as well as many other convienent functions that make work in PyMOL more productive..
pymol pdb shortcuts pymol-python aliases startup-script agile-pymol molecular-graphics pymol-plugin molecular-artwork biomolecular-artwork structural-bioinformatics protein-structure-analysis pml scripting figure-making image-making efficient-programming agile-programming ergonomic-keyword-use
Language:Python 84
pymodproject / pymod
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
bioinformatics homology-modeling protein-sequences protein-structures pymol pymol-plugin sequence-alignments similarity-searches structural-alignments
Language:Python 82
BGI-SynBio / PyMOL-PUB
Rapid generation of high-quality structure figures for publication with PyMOL-PUB
manuscript-figures matplotlib pymol pymol-extension structure-alignment structure-clustering matplotlib-extension
Language:Python 79
paiardin / DockingPie
A Consensus Docking Plugin for PyMOL
molecular-modeling pymol pymol-extension pymol-plugin ligand molecular molecular-docking molecular-dynamics
Language:Python 76
Valdes-Tresanco-MS / AMDock
(Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina
amdock docking autodock autodock4zn vina pymol scoring
Language:Python 73
AMDock-win
Valdes-Tresanco-MS / AMDock-win
(Windows) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina
amdock vina autodock4 pymol autodock4zn docking
Language:Python 67
ding-lab / hotspot3d
3D hotspot mutation proximity analysis tool
mutations perl 3d-proximity proximity-search clustering protein-structure hotspot analysis cancer genomic disease drug ensembl uniprot blat hgnc pymol drugport drugbank
Language:Perl 49
MooersLab / pymolsnips
Pymolsnips is a library of PyMOL scripting language code fragments for several popular text editors.
pymol pymol-snippets snippets pml autocompletion snippet-library pymol-snippet-library code-fragments pymol-code-fragments molecular-artwork text-editors vsc pymol-macro-language st3 tab-triggers textmate sublime-text-3 atom cudatext gedit
Language:Vim Snippet 45
PyVibMS
smutao / PyVibMS
A PyMOL plugin for visualizing vibrations in molecules and solids
pymol-plugin vibrational-spectroscopy quantum-chemistry theoretical-chemistry computational-physics pymol computational-chemistry
Language:Python 43
liyigerry / gmx
molecular dynamics simulation and analysis. 分子动力学模拟和分析。
gromacs md plumed pymol
Language:Jupyter Notebook 41
ferritin-bio / ferritin
protein utilities in Rust
proteins pymol rust
Language:Rust 32
wrf / pdbcolor
Python code to color a PDB structure based on parameters from a multiple sequence alignment
protein protein-structure evolution visualization pymol pdb-structure raxml phylobayes
Language:Python 32
patonlab / wSterimol
Generate Boltzmann-weighted Sterimol Steric Parameters for Conformationally-Flexible Substituents
sterimol sterics qsar pymol conformational-analysis organic-chemistry steric-parameters pymol-plugin sterimol-parameters
Language:Python 30
BioComputingUP / ring-pymol
This is the public repository for the RING PyMOL plugin developed by the BioComputing UP laboratory at the University of Padua
bioinformatics pymol plugin
Language:Python 29
MichelaNGLo-app
matteoferla / MichelaNGLo-app
A web app to convert a PyMOL PSE file or PDB file to a easy to implement NGL.js view that can be implemented easily on any site
pymol ngl pdb website app converter protein-structure protein
Language:Mako 28
insilichem / esigen
:memo::sparkles: Generate supporting information documents for your computational chemistry manuscripts - Documentation: https://esigen.readthedocs.io
computational-chemistry publication flask pymol webgl molecular-graphics
Language:JavaScript 21
smsaladi / pymol_viridis
Colorblind-friendly, perceptually uniform palettes for pymol
pymol visualization viridis palettes structural-biology colormap
Language:Python 20
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 19
felixplasser / qc_pymol
Scripts for using pymol together with quantum chemistry programs
quantum-chemistry electrostatic-potentials pymol
Language:Python 18
urban233 / PySSA
Python rich client for visual protein Sequence to Structure Analysis
protein-structure-analysis pymol python3 protein-structure-prediction
Language:Python 18
StructureAnalyzer
Cardypro / StructureAnalyzer
A program analyzing 3D protein structures from PDB to generate 2D binding motifs
chemistry pdb 3d-to-2d supramolecular protein-ligand-interactions pymol ligand protein binding-motifs
Language:Python 15
mtplr / pyMol-cookbook
Some notes (cookbook) for pyMol. Protein Crystallography course.
pymol protein-structure protein-ligand-interactions cookbook protein-stability
15
quantaosun / Pymol_Script
A python script for PyMol to make protein-ligand interaction images.
protein-ligand-docking pymol python-script
Language:Python 15
AHoJ-project
cusbg / AHoJ-project
:wave: Webserver & command-line tool for search of APO (unbound) protein structures from HOLO (bound) forms and vice versa. http://apoholo.cz
bioinformatics alignment python pymol molstar structural-bioinformatics pdb mmcif rest-api webapp apo-holo fastapi protein-structure proteins protein-data-bank structural-biology protein-ligand-complex computational-biology drug-discovery
14
filipsPL / CADD-PW
Computer Aided Drug Design / Komputerowe Wsparcie Projektowania Leków
cadd drug-discovery drug-design leki pymol knime marvin
Language:Python 12
Fluorescence-Tools / LabelLib
Library for coarse-grained simulations of probes flexibly coupled to biomolecules.
pymol fluorescence fret science-research simulation-toolkit accessible-volumes
Language:C++ 9
unizar-flav / PyViewDock
Docking viewer plug-in for PyMOL
pymol pymol-plugin docking bioinformatics proteins pdb
Language:Python 9
BIOS-IMASL / Azahar
A PyMOL plugin for construction, visualization and analysis of glycan molecules. https://www.ncbi.nlm.nih.gov/pubmed/27549814
pymol glycoinformatics plugin
Language:Python 8
MooersLab / orgpymolpysnips
Supports the use of PyMOL in literate programming in org-mode, which is best run in Emacs.
org-mode emacs literate-programming pymol molecular-graphics org-babel emacs-jupyter pdb protein mmcif
Language:YASnippet 8
exTerEX / pymol-ramachandran
A simple script to generate Ramachandran plot from Pymol.
pymol pymol-plugin ramachandran-plot ramachandran matplotlib-pyplot graphics figures
Language:Python 6
GiovanniMerici / Autodock-Vina
Simple pipeline to execute molecular docking experiments
autodock-vina docking molecular-biology molecular-docking p2rank pymol pymol-python structural-biology
Language:Jupyter Notebook 6
MooersLab / colabpymolpysnips
Library of PyMOL Python snippets for Google Colab.
colab-notebook notebook pymol protein protein-structure colab literate-programming python molecular biomolecular-structure code-fragments code-snippets ribbon-diagrams grayscale ca-trace molecular-surface drug-molecules ligand-binding-sites molecular-graphics
Language:Jupyter Notebook 6
zmactep / pymol-gpt
Fast and dirty GPT injection into PyMOL
gpt plugin pymol
Language:Python 6