pymol | Topic | Ecosyste.ms: Repos

Topic: "pymol"

rdk/p2rank

P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

Language: Groovy - Size: 675 MB - Last synced at: 13 days ago - Pushed at: 30 days ago - Stars: 304 - Forks: 37

cgohlke/pymol-open-source-wheels

Pymol-open-source wheels for Python on Windows.

Language: Python - Size: 56.6 KB - Last synced at: 18 days ago - Pushed at: 3 months ago - Stars: 114 - Forks: 14

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..

Language: Python - Size: 29.1 MB - Last synced at: 25 days ago - Pushed at: 12 months ago - Stars: 75 - Forks: 16

BGI-SynBio/PyMOL-PUB

Rapid generation of high-quality structure figures for publication with PyMOL-PUB

Language: Python - Size: 127 MB - Last synced at: 22 days ago - Pushed at: 6 months ago - Stars: 69 - Forks: 4

pymodproject/pymod

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

Language: Python - Size: 1.69 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 69 - Forks: 19

Valdes-Tresanco-MS/AMDock

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

Language: Python - Size: 19.8 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 67 - Forks: 16

paiardin/DockingPie

A Consensus Docking Plugin for PyMOL

Language: Python - Size: 212 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 61 - Forks: 12

Valdes-Tresanco-MS/AMDock-win

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

Language: Python - Size: 110 MB - Last synced at: 12 months ago - Pushed at: over 2 years ago - Stars: 54 - Forks: 19

ding-lab/hotspot3d

3D hotspot mutation proximity analysis tool

Language: Perl - Size: 1.11 GB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 44 - Forks: 26

smutao/PyVibMS

A PyMOL plugin for visualizing vibrations in molecules and solids

Language: Python - Size: 2.81 MB - Last synced at: 6 days ago - Pushed at: 7 months ago - Stars: 42 - Forks: 8

MooersLab/pymolsnips

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

Language: Vim Snippet - Size: 103 MB - Last synced at: 24 days ago - Pushed at: 12 months ago - Stars: 41 - Forks: 5

liyigerry/gmx

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

Language: Jupyter Notebook - Size: 28.6 MB - Last synced at: 15 days ago - Pushed at: over 5 years ago - Stars: 39 - Forks: 9

cbalbin-bio/pymol-color-alphafold

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

Language: Python - Size: 1.88 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 33 - Forks: 13

patonlab/wSterimol

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

Language: Python - Size: 989 KB - Last synced at: 25 days ago - Pushed at: almost 3 years ago - Stars: 29 - Forks: 10

ferritin-bio/ferritin

protein utilities in Rust

Language: Rust - Size: 57.6 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 28 - Forks: 2

BioComputingUP/ring-pymol

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

Language: Python - Size: 9.6 MB - Last synced at: 25 days ago - Pushed at: 3 months ago - Stars: 25 - Forks: 5

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

Language: Mako - Size: 107 MB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 25 - Forks: 4

wrf/pdbcolor

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

Language: Python - Size: 15.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 24 - Forks: 5

insilichem/esigen

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

Language: JavaScript - Size: 6.07 MB - Last synced at: 2 days ago - Pushed at: over 6 years ago - Stars: 21 - Forks: 1

MooersLab/EasyPyMOL

Script to facilitate the making of horizontal scripts

Language: Python - Size: 646 KB - Last synced at: 25 days ago - Pushed at: 11 months ago - Stars: 16 - Forks: 18

urban233/PySSA

Python rich client for visual protein Sequence to Structure Analysis

Language: Python - Size: 335 MB - Last synced at: 12 days ago - Pushed at: 25 days ago - Stars: 13 - Forks: 1

quantaosun/Pymol_Script

A python script for PyMol to make protein-ligand interaction images.

Language: Python - Size: 41 KB - Last synced at: 1 day ago - Pushed at: 24 days ago - Stars: 11 - Forks: 2

filipsPL/CADD-PW

Computer Aided Drug Design / Komputerowe Wsparcie Projektowania Leków

Language: Python - Size: 58.2 MB - Last synced at: 19 days ago - Pushed at: 3 months ago - Stars: 11 - Forks: 1

Cardypro/StructureAnalyzer

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

Language: Python - Size: 4.61 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 11 - Forks: 4

felixplasser/qc_pymol

Scripts for using pymol together with quantum chemistry programs

Language: Python - Size: 34.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 1

MooersLab/orgpymolpysnips

Supports the use of PyMOL in literate programming in org-mode, which is best run in Emacs.

Language: YASnippet - Size: 1.6 MB - Last synced at: 25 days ago - Pushed at: 12 months ago - Stars: 9 - Forks: 0

Fluorescence-Tools/LabelLib

Library for coarse-grained simulations of probes flexibly coupled to biomolecules.

Language: C++ - Size: 1.1 MB - Last synced at: 1 day ago - Pushed at: about 4 years ago - Stars: 9 - Forks: 3

smsaladi/pymol_viridis

Colorblind-friendly, perceptually uniform palettes for pymol

Language: Python - Size: 1.92 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 8 - Forks: 3

BIOS-IMASL/Azahar

A PyMOL plugin for construction, visualization and analysis of glycan molecules. https://www.ncbi.nlm.nih.gov/pubmed/27549814

Language: Python - Size: 138 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 7

zmactep/pymol-gpt

Fast and dirty GPT injection into PyMOL

Language: Python - Size: 863 KB - Last synced at: 20 days ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 0

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

Size: 5.7 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 5 - Forks: 1

MooersLab/colabpymolpysnips

Library of PyMOL Python snippets for Google Colab.

Language: Jupyter Notebook - Size: 2.41 MB - Last synced at: 25 days ago - Pushed at: 12 months ago - Stars: 5 - Forks: 9

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.

Language: HTML - Size: 286 MB - Last synced at: 11 months ago - Pushed at: almost 7 years ago - Stars: 5 - Forks: 3

GoetzParsiegla/Smina-plugin

This is a plugin for PyMol 2.x to use the vina/Autodock fork SMINA under Windows 10 or 11 with the wsl2 linux subsystem installed.

Language: Python - Size: 58.6 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 4 - Forks: 2

mmagnus/PyMOL4Spliceosome

Structures of the spliceosome processed to be easily viewed with PyMOL

Size: 16.7 MB - Last synced at: 12 months ago - Pushed at: almost 3 years ago - Stars: 4 - Forks: 0

atfrank/PyShifts

Pyshifts: A Pymol Plugin for Chemical Shift-Based Analysis of Biomolecular Ensembles

Language: Python - Size: 51.9 MB - Last synced at: 12 months ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 0

vegetablejuiceftw/coronavirus-begone

A Colab notebook explaining the pipeline for smile format, openbabel, autodock vina, pymol and more

Language: Jupyter Notebook - Size: 1.29 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 0

zhentg/GShare

Collaboration and sharing will make our research better!

Language: Python - Size: 117 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 3 - Forks: 1

SerenaRosi/SerenaRosi

SerenaRosi's GitHub page

Size: 68.4 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 3 - Forks: 0

MooersLab/colabOpenSourcePyMOLpySnips

Code snippets for colab-notebooks running open-source PyMOL

Language: Jupyter Notebook - Size: 2.23 MB - Last synced at: 24 days ago - Pushed at: 12 months ago - Stars: 3 - Forks: 1

MooersLab/PyMOLwallhangings

Protocol for making large scale images to be framed or for background images of posters.

Language: HTML - Size: 277 KB - Last synced at: 24 days ago - Pushed at: 12 months ago - Stars: 3 - Forks: 0

MooersLab/MooersLab

Landing page for MooersLab repository

Size: 1020 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

unizar-flav/PyViewDock

Docking viewer plug-in for PyMOL

Language: Python - Size: 1.39 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

RUBi-ZA/pyMODE-TASK

MODE-TASK plugin for PyMOL

Language: C++ - Size: 9.18 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 1

r4dbot/Biomolecular-simulation

Compilations of hands-on project Biomolecular simulations

Language: Python - Size: 139 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 0

asterlingchem/Tutorials

A repository containing tutorials for electronic structure analysis

Size: 1.36 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 0

ArturKlauser/pymol-pdb-plugin

PDB plugin for PyMOL

Language: Python - Size: 5.45 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 0

thibaudcolas/moulinette

Bioinformatics (biochemistry) data processing scripts for NMR, and protein data analysis (PyMOL)

Language: Python - Size: 75.2 KB - Last synced at: 7 days ago - Pushed at: about 7 years ago - Stars: 3 - Forks: 0

JMB-Scripts/AR-Structural-Biology

Augmented Reality object for biochemistry

Language: HTML - Size: 350 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 0

GiovanniMerici/Autodock-Vina

Simple pipeline to execute molecular docking experiments

Language: Jupyter Notebook - Size: 3.17 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

lucaspalmeira/bioinfo

Guia de programas e ferramentas de bioinformática e química computacional

Size: 16.6 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

MooersLab/pymolrc

Blaine's pymolrc file, the configuration file for the molecular graphics program.

Size: 5.86 KB - Last synced at: 24 days ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

tmp-production/ProteinViewer

A protein visualization system based on Unreal Engine 4.

Language: C++ - Size: 81.7 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

exTerEX/pymol-ramachandran

A simple script to generate Ramachandran plot from Pymol.

Language: Python - Size: 1.78 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1

aziza-calm/ppfmft

It is a plugin for PyMol that runs fmft

Language: Python - Size: 24.7 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 1

urban233/pymol-open-source-macos-build

Unofficial binary wheels for the open-source version of PyMOL, (including an updated menu stylesheet and an alternative splash screen) tailored for Python on macOS.

Language: C - Size: 19.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

urban233/pymol-open-source-linux-build

Unofficial binary wheels for the open-source version of PyMOL, (including an updated menu stylesheet and an alternative splash screen) tailored for Python on GNU Linux.

Language: Python - Size: 21.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

flexycode/BIOF-101

💫 BIOINFORMATICS for Drug Development

Size: 11.7 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

urban233/pymol-open-source-windows-build

Unofficial binary wheels for the open-source version of PyMOL, (including an updated menu stylesheet and an alternative splash screen) tailored for Python on Windows.

Language: Python - Size: 54.9 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

GiatrasKon/Algorithms-in-Structural-Bioinformatics-Assignments

Assignments from the 'Algorithms in Structural Bioinformatics' graduate course, exploring RNA folding, molecular conformational analysis, and protein structure comparison using Python and bioinformatics tools.

Language: Jupyter Notebook - Size: 6.61 MB - Last synced at: 25 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

zachcp/pseutils 📦

Make pymol session files vieweable on the web

Language: Rust - Size: 3.21 MB - Last synced at: 6 days ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

dacarlin/pymol-powerpack

A powerup for your PyMOL

Language: Python - Size: 2.93 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

MooersLab/pymolpysnips

The pymolsnips rewritten in Python. This Python enables direct interaction with the pymol api from other Python environments like electronic notebooks (e.g. Jupyter Notebooks), IDEs, and literate programming documents (e.g., Rmarkdown, org-mode ).

Language: Python - Size: 3.69 MB - Last synced at: 24 days ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

MooersLab/ACA2022

Slideshow to talk in August 2022 at 72nd Annual Meeting of the American Crystallographic Association

Size: 3.93 MB - Last synced at: 24 days ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

MooersLab/rstudiopymolpysnips

PyMOL snippet library is written in Python for use in RStudio via the R reticulate package and the PyMOL Python API.

Language: Vim Snippet - Size: 224 MB - Last synced at: 24 days ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

MooersLab/taggedpymolpysnips

PyMOL Python Script Writing with Code Templates in Jupyter notebooks with JupyterLab using the Elyra extension

Language: Jupyter Notebook - Size: 40.5 MB - Last synced at: 24 days ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0

atfrank/RNACavityMiner

Classifiers to Mine For Ligandable Binding Cavity in RNA

Language: Python - Size: 257 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 2

quantaosun/webdock

Open-Sourced. Easy docking in your browser without any login requirement. Post processing and interaction diagram included.

Language: Jupyter Notebook - Size: 6.62 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

JamesABaker/pymolrc_custom

.pymolrc is a pymol config that generates high quality ray traced images.

Language: Shell - Size: 1.64 MB - Last synced at: 15 days ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

SerenaRosi/PyMOL-toolbox

Language: Python - Size: 36.1 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

tsj5/APBS_Qt_plugin

Demo/experimental port of APBS plugin to PyQt for PyMOL 2.x.

Language: Python - Size: 459 KB - Last synced at: 11 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

caricato-ku/Stilde-Interpretation-and-Visualization

A program to sort and analyze large amounts of specific rotation analysis data. Then, using PyMol to superimpose vectors from the sorted data set onto molecules

Language: Python - Size: 1.02 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 1

GoetzParsiegla/Dipolemoment-plugin

This is a plugin for PyMol 2.x to calculate and show the dipole moment vector of a proteine structure in pdb format.

Language: Python - Size: 11.7 KB - Last synced at: 6 months ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

scatter3d/noodle-strut

noodle-strut is an interactive 3D printing structural support module for PyMOL

Language: Python - Size: 3.73 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 1

vcentfu/BioInfoProteins

[Bioinformatics] Identification de motifs structuraux dans les protéines

Language: Python - Size: 22.3 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

smutao/Three-Arm-Turnstile-Assistant

PyMOL plugin to modify molecular structure via turnstile rotation

Language: Python - Size: 18.6 KB - Last synced at: 6 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

cbalbin-bio/pymol-map-pocket

PyMOL extension to map a protein pocket, generated from PockDrug, to the full protein structure.

Language: Python - Size: 6.27 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

ElsevierSoftwareX/SOFTX_2020_149

Pmlbeta: a PyMOL extension for building β-amino acid insertions and β-peptide sequences. To cite this software publication: https://www.sciencedirect.com/science/article/pii/S2352711020303678

Language: Python - Size: 211 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

KimJR/DrugDesign

PyMOL

Language: Python - Size: 656 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1

oserve/PyNMR

Nuclear Magnetic Resonance (NMR) Spectroscopy structural data visualization tools extensions for Pymol

Language: Python - Size: 2.95 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 1

hkabbech/AA_inventory

Inventory of amino acids present on the surface of peripheral proteins of a same family

Language: Python - Size: 10.3 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 1

amanchandra333/bioinformatics

Assignments of Bioinformatics Lab

Language: C - Size: 1.07 MB - Last synced at: almost 2 years ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 2

Noora-Alhajeri/Molecular-Visualization-PyMOL

Visualizing the 6KIX Histone Protein using PyMOL – includes annotated movie scenes.

Size: 2.81 MB - Last synced at: about 13 hours ago - Pushed at: about 14 hours ago - Stars: 0 - Forks: 0

Tushar98644/Ribo-Replicator

Generation and visualization of 3d protein sequences

Language: TypeScript - Size: 811 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

keni105/select_residue_water_residue_combined.py

This tool is particularly useful for studying water-mediated interactions in protein complexes and macromolecular structures.

Language: Python - Size: 9.77 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

keni105/align_and_color_with_selection.py

The align_and_color_with_selection.py script is a PyMOL plugin designed to streamline the comparison of two structural models. It performs structural alignment, highlights differing residues, and creates selections for these residues, making it a valuable tool for structural biologists analyzing homologous structures or variants.

Language: Python - Size: 0 Bytes - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0