pymol

There are 4 repositories under pymol topic.

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 224
pymodproject / pymod
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
pymol bioinformatics sequence-alignments structural-alignments homology-modeling similarity-searches pymol-plugin protein-structures protein-sequences
Language:Python 70
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 63
paiardin / DockingPie
A Consensus Docking Plugin for PyMOL
ligand molecular molecular-docking molecular-dynamics molecular-modeling pymol pymol-extension pymol-plugin
Language:Python 61
Valdes-Tresanco-MS / AMDock
(Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina
amdock docking autodock autodock4zn vina pymol scoring
Language:Python 57
AMDock-win
Valdes-Tresanco-MS / AMDock-win
(Windows) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina
amdock vina autodock4 pymol autodock4zn docking
Language:Python 54
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 49
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 45
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 40
BGI-SynBio / PyMOL-PUB
Rapid generation of high-quality structure figures for publication with PyMOL-PUB
manuscript-figures matplotlib matplotlib-extension pymol pymol-extension structure-alignment structure-clustering
Language:Python 36
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 35
cgohlke / pymol-open-source-wheels
Pymol-open-source wheels for Python on Windows
pymol pymol-python python wheels windows
Language:Python 31
liyigerry / gmx
molecular dynamics simulation and analysis. 分子动力学模拟和分析。
md gromacs pymol plumed
Language:Jupyter Notebook 31
wrf / pdbcolor
Python code to color a PDB structure based on parameters from a multiple sequence alignment
evolution pdb-structure phylobayes protein protein-structure pymol raxml visualization
Language:Python 30
bobbypaton / 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 24
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 24
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 20
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 plugin pymol
Language:Python 19
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 15
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 14
mtplr / pyMol-cookbook
Some notes (cookbook) for pyMol. Protein Crystallography course.
cookbook protein-ligand-interactions protein-stability protein-structure pymol
14
felixplasser / qc_pymol
Scripts for using pymol together with quantum chemistry programs
electrostatic-potentials pymol quantum-chemistry
Language:Python 12
filipsPL / CADD-PW
Computer Aided Drug Design / Komputerowe Wsparcie Projektowania Leków
cadd drug-discovery drug-design leki pymol knime marvin
Language:Python 11
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
smsaladi / pymol_viridis
Colorblind-friendly, perceptually uniform palettes for pymol
colormap palettes pymol structural-biology viridis visualization
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
glycoinformatics plugin pymol
Language:Python 7
MooersLab / orgpymolpysnips
Supports the use of PyMOL in literate programming in org-mode, which is best run in Emacs.
emacs emacs-jupyter literate-programming mmcif molecular-graphics org-babel org-mode pdb protein pymol
Language:YASnippet 6
charlesdavid / JED
JED is a program for performing Essential Dynamics of protein trajectories written in Java. JED is a powerful tool for examining the dynamics of proteins from trajectories derived from MD or Geometric simulations. Currently, there are two types of PCA: distance-pair and Cartesian, and three models: COV, CORR, and PCORR.
pca-analysis subspace-identification covariance-matrix correlation-matrices essentialmode principal-components dynamical-modeling correlation-measures pymol free-energy kernel-density-estimation eigen-vector-decomposition
Language:HTML 5
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
5
unizar-flav / PyViewDock
Docking viewer plug-in for PyMOL
pymol pymol-plugin docking bioinformatics proteins pdb
Language:Python 5
asterlingchem / Tutorials
A repository containing tutorials for electronic structure analysis
electronic-structure-calculations electronic-structure quantum-chemistry non-covalent-interactions electron-density orca-quantum-chemistry orca pymol
4
atfrank / PyShifts
Pyshifts: A Pymol Plugin for Chemical Shift-Based Analysis of Biomolecular Ensembles
chemical-shift pymol-plugin pymol error-analysis
Language:Python 4
PyMOL4Spliceosome
mmagnus / PyMOL4Spliceosome
Structures of the spliceosome processed to be easily viewed with PyMOL
bioinformatics pymol rna rna-tools spliceosome structural
4
RUBi-ZA / pyMODE-TASK
MODE-TASK plugin for PyMOL
pca nma molecular-dynamics normal-modes mds tsne-algorithm pymol pymol-plugin pymode-task tkinter principal-component-analysis protein-structure protein md pdb rmsd trajectory-analysis molecular-dynamics-simulation python
Language:C++ 4
vegetablejuiceftw / coronavirus-begone
A Colab notebook explaining the pipeline for smile format, openbabel, autodock vina, pymol and more
smile-string autodock-vina pymol openbabel colab-notebook python3 coronavirus
Language:Jupyter Notebook 4
zmactep / pymol-gpt
Fast and dirty GPT injection into PyMOL
gpt plugin pymol
Language:Python 4