molecular-docking

There are 13 repositories under molecular-docking topic.

ccsb-scripps / AutoDock-GPU
AutoDock for GPUs and other accelerators
autodock4 cuda gpu-computing molecular-docking multicore-cpu opencl
Language:C++ 418
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.
molecular-docking autodock autodock-vina ledock mdanalysis rdkit openbabel cheminformatics computational-biology jupyter-notebook py3dmol protein protein-structure drug-discovery drug-repurposing drug-design
Language:Jupyter Notebook 260
MolecularAI / DockStream
DockStream: A Docking Wrapper to Enhance De Novo Molecular Design
reinforcement-learning jupyter-notebook chemoinformatics molecular-docking denovo-design astrazeneca
Language:Python 109
awesome-molecular-docking
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.
ai-aided-drug-discovery awesome drug-discovery molecular-docking paper-list bioinformatics machine-learning protein-protein-interaction molecular-dynamics binding generative-model drug-design equivariant-representations drug-protein-interactions geometric-deep-learning awesome-list deep-learning optimal-transport protein-ligand-docking drugai
96
RMeli / spyrmsd
📐 Symmetry-corrected RMSD in Python
rmsd symmetry cadd computational-biology computational-chemistry computer-aided-drug-design docking drug-discovery molecular-docking
Language:Python 89
coleygroup / pyscreener
pythonic interface to virtual screening software
virtual-screening computational-biology molecular-docking distributed-computing ray
Language:Python 86
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]
docking molecular-docking virtual-screening ligand-screening drug-discovery protein-drug-interactions protein-ligand-docking protein-ligand-interactions protein-ligand-binding-conformation protein-ligand-interfaces cxx cxx11 python python3
Language:C++ 68
paiardin / DockingPie
A Consensus Docking Plugin for PyMOL
molecular-modeling pymol pymol-extension pymol-plugin ligand molecular molecular-docking molecular-dynamics
Language:Python 65
biocheming / watvina
implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking
autodock-vina molecular-docking water-docking drug-design watvina pharmacophore
Language:Jupyter Notebook 53
RyanZR / labodock
LABODOCK: A Colab-Based Molecular Docking Tools
autodock-vina cheminformatics drug-design google-colab molecular-docking plip virtual-screening
Language:Jupyter Notebook 42
ci-lab-cz / easydock
molecular-docking
Language:Python 38
DockM8
DrugBud-Suite / DockM8
All in one Structure-Based Virtual Screening workflow based on the concept of consensus docking.
cheminformatics cheminformatics-and-compchem compchem computational-chemistry docking drug-design drug-discovery molecular-docking molecular-modeling protein-ligand-interactions sbvs virtual-screening
Language:Jupyter Notebook 36
radifar / PyPLIF-HIPPOS
HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS
molecular-docking autodock-vina interaction-fingerprinting virtual-screening drug-discovery
Language:Python 28
MolecularAI / DockStreamCommunity
reinforcement-learning chemoinformatics jupyter-notebook denovo-design astrazeneca molecular-docking
Language:Jupyter Notebook 26
plainerman / DiffDock-Pocket
Implementation of DiffDock-Pocket: Diffusion for Pocket-Level Docking with Side Chain Flexibility
diffusion-models drug-discovery generative-ai machine-learning molecular-docking computational-biology
Language:Python 23
drug-design / course
drugdesign.org source of truth
bioinformatics cheminformatics database-searching drug-design drug-discovery drugs library-design molecular-dynamics molecular-modeling molecular-similarity protein-ligand qsar structure-activity-relationships molecular-docking
19
annapurna
filipsPL / annapurna
AnnapuRNA: a scoring function for predicting RNA-small molecule interactions.
rna scoring ligand molecular-docking small-molecules
Language:Python 19
NRGlab / FlexAID
Flexible Artificial Intelligence Docking
docking molecular-docking protein-ligand-docking ligand-screening protein-ligand-binding-conformation protein-ligand-interactions protein-ligand-interfaces
Language:C 16
jp43 / DockBox
Python package to facilitate the use of popular docking software
consensus-algorithm molecular-docking scoring-algorithm wrapper-library
Language:Python 15
BIMSBbioinfo / CompassDock
Official Implementation of CompassDock
binding-affinity drug-discovery drug-target-interactions molecular-biology molecular-docking protein-ligand-interactions
Language:Python 14
ailabstw / DockCoV2
A molecular docking pipeline for the drug database against SARS-CoV2
sars-cov-2 drug-database molecular-docking
Language:JavaScript 13
wudangt / awesome-molecular-modeling-and-drug-discovery
A curated list of awesome Molecular Modeling And Drug Discovery 🔥
molecular-modeling alphafold alphafold2 bioinformatics drug-discovery protein-engineering protein-sequence protein-structure structural-biology molecular-docking molecular-evolution molecular-generation
10
docktgrid
gmmsb-lncc / docktgrid
Generate customized voxel representations of protein-ligand complexes using GPU.
deep-learning molecular-docking scoring-functions binding-affinity virtual-screening voxel-grid
Language:Python 9
OtimusOne / AFPAP
AlphaFold-based Protein Analysis Pipeline
bioinformatics molecular-docking multiqc nextflow pdb pipeline protein python sequence-analysis structure-analysis
Language:Python 8
rribeiro-sci / pygomodo
GPCRs modeling and docking with python
bioinformatics bioinformatics-pipeline bioinformatics-tool gpcr homology-modeling molecular-docking
Language:Python 8
suleymanselim / MolecularDockingTutorials
Molecular docking scripts for virtual screening studies
molecular-docking drug-discovery virtual-screening-studies molecular-docking-scripts
Language:Perl 7
thuxugang / opus_rota5
OPUS-Rota5: A Highly Accurate Protein Side-chain Modeling Method with 3D-Unet and RotaFormer
molecular-docking protein-side-chain-modeling protein-structure-prediction
Language:Python 7
primaryodors / primarydock
PrimaryOdors.org molecular docker.
gpcr molecular-docking molecular-viewer molecular-visualization olfaction path-based-docking protein-function-prediction protein-ligand-interactions side-chain-flexion side-chain-orientation
Language:C++ 6
mahsasheikh / DrugGen
DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback
drug-design drug-repurposing gpt-2 large-language-model molecular-docking reinforcement-learning transformers
Language:Python 5
RyanZR / LaBOX
LaBOX: A Grid Box Calculation Tool for Molecular Docking
autodock-vina grid-box molecular-docking search-space chemoinformatics drug-design
Language:Python 5
biodasturchi / docs
📡 Biodasturchi blog website
typescript vitepress-blog vue molecular-biology molecular-docking molecular-dynamics
Language:TypeScript 4
bachelor-thesis
gomax22 / bachelor-thesis
LaTeX Bachelor's Thesis
computational-chemistry latex molecular-docking molecular-interactions convolutional-neural-networks deep-learning
Language:TeX 4
marcin-cieslak / mao-qsar
QSAR models and data used for MAO-A and MAO-B virtual screening.
computer-aided-drug-design machine-learning molecular-docking qsar
Language:Python 4
volkamerlab / MolDockLab
MolDockLab is a data-driven workflow developed to identify the best balanced consensus Structure-Based Virtual Screening (SBVS) workflow for a target of interest.
molecular-docking sbvs virtual-screening consensus-docking
Language:Jupyter Notebook 4
azminewasi / Awsome-CompBio-Bioinformatics
A curated list of FREE courses available online from top universities of the world on Computational Biology and Bioinformatics.
bioinformatics bioinformatics-analysis computational-biology computational-chemistry computational-geometry drug-design drug-discovery drug-repurposing molecular-biology molecular-docking protein-folding protein-protein-interaction protein-sequences protein-structure protein-structure-prediction
3
ucm-lbqc / polypharm
A Python-based library to perform IFD and MM/GBSA calculations on different targets using a polypharmacological approach.
computational-chemistry free-energy-calculations molecular-docking polypharmacology
Language:Python 3