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pymol

Here are 86 public repositories matching this 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.

java groovy machine-learning bioinformatics random-forest proteins pdb molecular-structures protein-structure protein-ligand-docking prediction pymol mmcif protein-ligand-interactions binding-sites ligand inverse-virtual-screening protein-surface structural-bioinformatics

Updated May 9, 2023
Groovy

pymodproject / pymod

PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.

bioinformatics pymol-plugin pymol protein-sequences sequence-alignments homology-modeling protein-structures structural-alignments similarity-searches

Updated Apr 6, 2023
Python

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..

Updated Jun 9, 2023
Python

ding-lab / hotspot3d

3D hotspot mutation proximity analysis tool

analysis cancer clustering perl protein-structure ensembl mutations pymol hgnc disease drug drugbank hotspot uniprot blat 3d-proximity proximity-search genomic drugport

Updated Mar 31, 2023
Perl

Valdes-Tresanco-MS / AMDock

Sponsor

(Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina

scoring pymol docking autodock vina amdock autodock4zn

Updated Sep 1, 2022
Python

cbalbin-bio / pymol-color-alphafold

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

bioinformatics structural-biology pymol-plugin protein-structure computational-biology pymol alphafold alphafold2

Updated Feb 18, 2022
Python

AMDock-win

Valdes-Tresanco-MS / AMDock-win

Sponsor

(Windows) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina

pymol docking vina amdock autodock4zn autodock4

Updated Aug 1, 2022
Python

paiardin / DockingPie

A Consensus Docking Plugin for PyMOL

pymol-plugin molecular-dynamics pymol molecular ligand molecular-modeling molecular-docking pymol-extension

Updated May 9, 2023
Python

MooersLab / pymolsnips

Pymolsnips is a library of PyMOL scripting language code fragments for several popular text editors.

Updated Sep 28, 2022
Vim Snippet

PyVibMS

smutao / PyVibMS

A PyMOL plugin for visualizing vibrations in molecules and solids

pymol-plugin computational-chemistry pymol computational-physics quantum-chemistry vibrational-spectroscopy theoretical-chemistry

Updated Jan 30, 2022
Python

liyigerry / gmx

molecular dynamics simulation and analysis. 分子动力学模拟和分析。

pymol gromacs md plumed

Updated Oct 3, 2019
Jupyter Notebook

bobbypaton / wSterimol

Generate Boltzmann-weighted Sterimol Steric Parameters for Conformationally-Flexible Substituents

pymol-plugin pymol organic-chemistry conformational-analysis qsar sterimol sterics steric-parameters sterimol-parameters

Updated Jun 21, 2022
Python

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

converter website app pdb protein-structure protein pymol ngl

Updated Jan 31, 2023
Mako

wrf / pdbcolor

Python code to color a PDB structure based on parameters from a multiple sequence alignment

visualization evolution protein-structure protein pymol raxml phylobayes pdb-structure

Updated Feb 1, 2023
Python

insilichem / esigen

📝✨ Generate supporting information documents for your computational chemistry manuscripts - Documentation: https://esigen.readthedocs.io

flask webgl molecular-graphics computational-chemistry pymol publication

Updated Jan 23, 2019
JavaScript

BioComputingUP / ring-pymol

This is the public repository for the RING PyMOL plugin developed by the BioComputing UP laboratory at the University of Padua

plugin bioinformatics pymol

Updated May 14, 2023
Python

felixplasser / qc_pymol

Scripts for using pymol together with quantum chemistry programs

pymol quantum-chemistry electrostatic-potentials

Updated Apr 22, 2021
Python

MooersLab / EasyPyMOL

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

Updated Sep 26, 2022
Python

StructureAnalyzer

Cardypro / StructureAnalyzer

A program analyzing 3D protein structures from PDB to generate 2D binding motifs

chemistry pdb protein pymol protein-ligand-interactions ligand 3d-to-2d supramolecular binding-motifs

Updated Jul 18, 2021
Python

filipsPL / CADD-PW

Computer Aided Drug Design / Komputerowe Wsparcie Projektowania Leków

knime pymol drug-discovery marvin drug-design cadd leki

Updated Jan 10, 2023
Python

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