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Scindices / 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.

lang-python status-archived task-visualization role-application domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule interface-jupyter status-published scope-focused domain-drug-discovery task-docking method-physics entity-complex

Updated Oct 30, 2023
Jupyter Notebook

Scindices / molinfo-vienna--apo2ph4

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A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening

status-active lang-python interface-cli task-workflow role-application domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule status-published scope-focused domain-drug-discovery entity-complex method-rule-based task-pharmacophore

Updated May 22, 2025
Python

Scindices / ccsb-scripps--AutoDock-Vina

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AutoDock Vina

status-active lang-cpp interface-cli role-application domain-structural-biology entity-protein entity-small-molecule status-published status-packaged-conda scope-focused domain-drug-discovery task-docking method-physics entity-complex ecosystem-autodock

Updated Feb 25, 2026
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Scindices / SeonghwanSeo--PharmacoNet

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Official Github for "PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening" (Chemical Science)

status-active lang-python interface-cli method-deep-learning role-application domain-cheminformatics entity-protein entity-small-molecule interface-api status-published scope-focused domain-drug-discovery entity-complex interface-gpu task-pharmacophore

Updated Jul 15, 2025
Python

Scindices / ccsb-scripps--AutoGrid

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status-archived lang-c interface-cli role-application domain-structural-biology entity-protein entity-small-molecule status-published scope-focused domain-drug-discovery task-docking method-physics ecosystem-autodock task-featurization

Updated Dec 7, 2024
C++

Scindices / bytedance--AnewOmni

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Codes for our paper "Programming Biomolecular Interactions with All-Atom Generative Model"

status-active lang-python interface-cli method-deep-learning role-application domain-structural-biology entity-protein entity-small-molecule status-published scope-focused domain-drug-discovery entity-complex interface-gpu task-molecular-generation method-diffusion task-protein-design

Updated Jun 6, 2026
Python

Scindices / arneschneuing--DiffSBDD

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A Euclidean diffusion model for structure-based drug design.

status-active lang-python interface-cli method-deep-learning role-application domain-cheminformatics entity-protein entity-small-molecule status-published scope-focused domain-drug-discovery entity-complex interface-gpu task-molecular-generation method-diffusion method-geometric-learning

Updated Jun 25, 2025
Python

Scindices / volkamerlab--teachopencadd

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TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

status-active lang-python interface-cli task-workflow role-application domain-structural-biology domain-cheminformatics entity-protein entity-small-molecule interface-jupyter status-published status-packaged-pypi status-packaged-conda domain-drug-discovery method-rule-based scope-suite

Updated Jul 23, 2026
Jupyter Notebook

Scindices / RosettaCommons--RoseTTAFold

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This package contains deep learning models and related scripts for RoseTTAFold

lang-python status-archived interface-cli method-deep-learning role-application domain-structural-biology entity-protein status-published scope-focused entity-complex interface-gpu task-structure-prediction

Updated Feb 15, 2024
Python

Scindices / coleygroup--shepherd

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Training and inference code for ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design [ICLR 2025 oral]

entity-graph status-active lang-python interface-cli method-deep-learning role-application domain-cheminformatics entity-small-molecule interface-api status-published scope-focused domain-drug-discovery interface-gpu task-molecular-generation task-pharmacophore method-diffusion

Updated Mar 31, 2026
Python

Scindices / PKUGaoGroup--DSDP

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Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications.

status-active lang-python lang-cpp interface-cli method-deep-learning role-application domain-structural-biology entity-protein entity-small-molecule status-published scope-focused domain-drug-discovery task-docking task-binding-site method-physics entity-complex interface-gpu lang-cuda

Updated Jun 27, 2025
C++

Scindices / gnina--gnina

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A deep learning framework for molecular docking

status-active lang-cpp interface-cli method-deep-learning role-application domain-structural-biology entity-protein entity-small-molecule status-published scope-focused domain-drug-discovery task-docking method-physics entity-complex interface-gpu ecosystem-gnina lang-cuda

Updated Jun 29, 2026
C++

Scindices / lh3--bwa

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Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

status-active task-alignment lang-c domain-bioinformatics interface-cli role-application status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid entity-sequence domain-genomics

Updated Jul 25, 2026
C

Scindices / Discngine--fpocket

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fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software.