Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: molecular-docking

Repositories

Lambda-UFPB/PharMisa

Automated pipeline for pharmacophore based virtual screening using the interface of pharmit interactive exploration of chemical space and ADMET analysis using ADMETLAB 2.0 API

Language: Python - Size: 654 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

DrugBud-Suite/DockM8

All in one Structure-Based Vitual Screening workflow based on the concept of consensus docking.

Language: Jupyter Notebook - Size: 203 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 9 - Forks: 1

virtualscreenlab/BBB-ChT

Comparative In Silico Analysis of CNS-Active Molecules Targeting the Blood–Brain Barrier Choline Transporter for Alzheimer's Disease Therapy: A Case Study

Language: Jupyter Notebook - Size: 65.9 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 1 - Forks: 0

paiardin/DockingPie

A Consensus Docking Plugin for PyMOL

Language: Python - Size: 212 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 61 - Forks: 12

RMeli/spyrmsd

📐 Symmetry-corrected RMSD in Python

Language: Python - Size: 752 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 75 - Forks: 7

plainerman/DiffDock-Pocket

Implementation of DiffDock-Pocket: Diffusion for Pocket-Level Docking with Side Chain Flexibility

Language: Python - Size: 4 MB - Last synced: 29 days ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

gmmsb-lncc/docktgrid

Create customized voxel representations of protein-ligand complexes using GPU.

Language: Python - Size: 1.32 MB - Last synced: about 20 hours ago - Pushed: about 1 month ago - Stars: 7 - Forks: 2

ucm-lbqc/polypharm

A Python-based library to perform IFD and MM/GBSA calculations on different targets using a polypharmacological approach.

Language: Python - Size: 1.99 MB - Last synced: 3 days ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

This package facilitates molecular docking simulations aimed at analyzing interactions between a target biological system and a collection of potential drug molecules. By leveraging computational algorithms, it ranks these molecules based on docking scores and interaction energies, providing insights into their suitability as drug candidates.

Language: Python - Size: 1.75 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

MolecularAI/DockStream 📦

DockStream: A Docking Wrapper to Enhance De Novo Molecular Design

Language: Python - Size: 15.3 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 97 - Forks: 29

biocheming/watvina

implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking

Language: Jupyter Notebook - Size: 559 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 41 - Forks: 12

Thinklab-SJTU/awesome-molecular-docking

We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.

Size: 86.9 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 85 - Forks: 5

quantori/scip-dockinginterface

DockingInterface is a Python wrapper for open-source molecular docking programs: Autodock Vina, Smina, QVina2, and rDock.

Language: MATLAB - Size: 125 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

quantori/scip-rdock

rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. This fork adds changes to rDock that allow it to be a part of DockingFactory.

Language: C++ - Size: 19.9 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

quantori/scip-vina

AutoDock Vina is one of the fastest and most widely used open-source docking engines. It is based on a simple scoring function and rapid gradient-optimization conformational search. It was originally designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab. This fork of Vina adds changes that allow it to be a part of DockingFactory.

Language: C++ - Size: 105 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

quantori/scip-qvina

Quick Vina 2 is a fast and accurate molecular docking tool, attained at accurately accelerating AutoDock Vina. This fork of QVina 2 adds changes that allow it to run as part of DockingFactory.

Language: C++ - Size: 156 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

quantori/scip-smina

Smina is fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project. This fork of Smina adds changes that allow it to run as a part of DockingFactory.

Language: C++ - Size: 2.84 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

quantori/scip-dockingfactory

Docking Factory is a tool to automate molecular docking runs on an HPC cluster using the Dask framework. DockingFactory provides unified way of running molecular docking with different software backends: AutoDock Vina, Smina, Qvina2, and rDock.

Language: MATLAB - Size: 1.69 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

primaryodors/primarydock

PrimaryOdors.org molecular docker.

Language: C++ - Size: 179 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 3

filipsPL/annapurna

AnnapuRNA: a scoring function for predicting RNA-small molecule interactions.

Language: Python - Size: 278 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 19 - Forks: 5

ccsb-scripps/AutoDock-GPU

AutoDock for GPUs and other accelerators

Language: C++ - Size: 44.4 MB - Last synced: 2 months ago - Pushed: 3 months ago - Stars: 341 - Forks: 97

radifar/PyPLIF-HIPPOS

HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS

Language: Python - Size: 40.9 MB - Last synced: 26 days ago - Pushed: 10 months ago - Stars: 26 - Forks: 7

AngelRuizMoreno/Jupyter_Dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

Language: Jupyter Notebook - Size: 30.8 MB - Last synced: 3 months ago - Pushed: 7 months ago - Stars: 240 - Forks: 58

jp43/DockBox

Python package to facilitate the use of popular docking software

Language: Python - Size: 6.53 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 14 - Forks: 7

MolecularAI/DockStreamCommunity 📦

Language: Jupyter Notebook - Size: 9.2 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 25 - Forks: 11

wudangt/awesome-molecular-modeling-and-drug-discovery

A curated list of awesome Molecular Modeling And Drug Discovery 🔥

Size: 51.8 KB - Last synced: 20 days ago - Pushed: almost 2 years ago - Stars: 10 - Forks: 0

drug-design/course

drugdesign.org source of truth

Size: 2.1 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 11 - Forks: 3

suleymanselim/MolecularDockingTutorials

Molecular docking scripts for virtual screening studies

Language: Perl - Size: 1.8 MB - Last synced: 4 months ago - Pushed: over 4 years ago - Stars: 7 - Forks: 2

RyanZR/labodock

LABODOCK: A Colab-Based Molecular Docking Tools

Language: Jupyter Notebook - Size: 4.99 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 23 - Forks: 8

coleygroup/pyscreener

pythonic interface to virtual screening software

Language: Python - Size: 7.17 MB - Last synced: 3 months ago - Pushed: about 1 year ago - Stars: 75 - Forks: 30

rribeiro-sci/pygomodo

GPCRs modeling and docking with python

Language: Python - Size: 486 MB - Last synced: 26 days ago - Pushed: 4 months ago - Stars: 8 - Forks: 1

SerenaRosi/SerenaRosi

SerenaRosi's GitHub page

Size: 63.5 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

j-gorm/MathModel-FiberEater-2023-iDL-FCB-UANL

Mathematical Modeling from the "Fiber-Eater" project, for the iGEM Design League Competition 2023.

Language: Jupyter Notebook - Size: 4.61 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

lmorency/NRGsuite

The NRGsuite is a PyMOL plugin (GUI) for FlexAID

Language: Python - Size: 12.1 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 8

ailabstw/DockCoV2

A molecular docking pipeline for the drug database against SARS-CoV2

Language: JavaScript - Size: 8.13 MB - Last synced: 8 months ago - Pushed: over 3 years ago - Stars: 14 - Forks: 2

Chester75321/DockCoV2

A molecular docking pipeline for the drug database against SARS-CoV2

Language: JavaScript - Size: 7.8 MB - Last synced: 8 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

thuxugang/opus_rota5

OPUS-Rota5: A Highly Accurate Protein Side-chain Modeling Method with 3D-Unet and RotaFormer

Language: Python - Size: 25.7 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 2 - Forks: 2

rxdock/rxdock

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

Language: C++ - Size: 32.4 MB - Last synced: 8 months ago - Pushed: almost 2 years ago - Stars: 59 - Forks: 18

Sarah-Hesham-2022/Drug-Design-AutoDock-Tools-MBP-D-Ribose

Molecular docking is one of the molecular modeling methods that predicts the preferred orientation of one molecule (ligand) to another (receptor) when bound to each other to form a stable complex (lowest energy state).

Size: 20.1 MB - Last synced: 5 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

RyanZR/LaBOX

LaBOX: A Grid Box Calculation Tool for Molecular Docking

Language: Python - Size: 11.7 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 2 - Forks: 0

quantori/scip-dockingfactory-bundle

Language: Python - Size: 95.7 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

cbstanley/docking

A set of molecular docking tools and analysis

Language: Jupyter Notebook - Size: 600 KB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

biodasturchi/docs

📡 Biodasturchi blog website

Language: TypeScript - Size: 23.9 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 4 - Forks: 1

gandhi-group-biomolecular/docking-oxazolidinone-dataset

Structure availability for dataset used in oxazolidinone docking and virtual screening

Size: 714 KB - Last synced: 11 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

NRGlab/NRGsuite Fork of lmorency/NRGsuite

NRGsuite is a PyMOL plugin (GUI) for FlexAID

Language: Python - Size: 12.2 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 3 - Forks: 3

Related Keywords

molecular-docking 59 drug-discovery 18 virtual-screening 15 docking 12 bioinformatics 9 drug-design 7 autodock-vina 6 molecular-dynamics 6 computational-chemistry 6 molecular-modeling 6 protein-ligand-interactions 6 molecular-docking-scripts 6 python 6 protein-ligand-docking 5 opencl 4 computational-biology 4 chemoinformatics 4 cheminformatics 4 jupyter-notebook 3 autodock 3 machine-learning 3 autodock-gpu 3 structural-biology 3 deep-learning 3 reproducible-research 3 paper 3 ligand 3 protein-ligand-binding-conformation 3 protein 3 gpu 3 cpu 3 astrazeneca 2 denovo-design 2 reinforcement-learning 2 gpcr 2 hpc 2 dask 2 drug-database 2 sars-cov-2 2 consensus-algorithm 2 ligand-screening 2 scoring-functions 2 latex 2 protein-ligand-interfaces 2 computer-aided-drug-design 2 pymol-plugin 2 pymol-extension 2 pymol 2 qsar 2 protein-structure 2 cuda 2 sx-aurora-tsubasa 2 bioinformatics-pipeline 2 cxx11 1 distributed-computing 1 protein-drug-interactions 1 python3 1 active-sites 1 biology 1 multiqc 1 ray 1 bioinformatics-tool 1 homology-modeling 1 bioinformatics-tutorials 1 pymol-plugins 1 pymol-python 1 rmsd-algorithms 1 roc-curve 1 software-development 1 structural-bioinformatics 1 design-league 1 igem-competition 1 mathematical-modelling 1 protein-side-chain-modeling 1 protein-structure-prediction 1 cxx 1 nextflow 1 pdb 1 pipeline 1 sequence-analysis 1 structure-analysis 1 api 1 visualization 1 convolutional-neural-networks 1 molecular-interactions 1 cnn 1 customtkinter 1 tkinter 1 tkinter-gui 1 data-analysis 1 data-science 1 r-language 1 drug-target-interactions 1 blind-docking 1 computer-graphics-algorithms 1 d-ribose 1 escherichia-coli 1 mbp 1 receptor 1 receptor-ligand-interaction 1