#

entity-small-molecule

Here are 147 public repositories matching this topic...

Scindices / jax-md--jax-md

Differentiable, Hardware Accelerated, Molecular Dynamics

status-active lang-python method-deep-learning role-framework entity-small-molecule interface-api status-published status-packaged-pypi scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu entity-crystal task-md-engine task-ml-potential

Updated Jul 26, 2026
Jupyter Notebook

Scindices / ccsb-scripps--AutoGrid

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

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 / PatWalters--useful_rdkit_utils

Some useful RDKit functions

status-active role-library lang-python domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-packaged-pypi scope-focused domain-drug-discovery task-featurization ecosystem-rdkit

Updated Jun 1, 2026
Jupyter Notebook

Scindices / torchmd--torchmd

End-To-End Molecular Dynamics (MD) Engine using PyTorch

status-active lang-python method-deep-learning role-framework entity-small-molecule interface-api status-published status-packaged-pypi scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu task-md-engine task-ml-potential

Updated Apr 21, 2026
Python

Scindices / ccsb-scripps--AutoDock-Vina

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
C++

Scindices / datamol-io--datamol

Molecular Processing Made Easy.

entity-graph status-active role-library lang-python domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery task-featurization ecosystem-rdkit

Updated May 20, 2026
Python

Scindices / rxn4chemistry--rxnfp

Reaction fingerprints, atlases and classification. Code complementing our Nature Machine Intelligence publication on "Mapping the space of chemical reactions using attention-based neural networks" (http://rdcu.be/cenmd).

entity-graph role-library lang-python status-archived method-deep-learning domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi scope-focused task-featurization task-retrosynthesis

Updated Aug 12, 2021
HTML

Scindices / uibcdf--pharmacophoremt

A Pharmacophore MultiToolkit designed to simplify and streamline the detection, generation, analysis, comparison, and application of pharmacophore models in drug-design strategies.

status-active lang-python domain-cheminformatics method-chemoinformatics entity-protein entity-small-molecule interface-api status-published domain-drug-discovery entity-complex role-toolkit scope-suite task-pharmacophore ecosystem-molsys

Updated May 26, 2026
Jupyter Notebook

Scindices / RBVI--ChimeraX

Source code for molecular graphics program UCSF ChimeraX

status-active lang-python lang-cpp task-visualization interface-cli domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein entity-small-molecule interface-api status-published method-physics entity-complex scope-swissknife entity-nucleic-acid interface-gui role-viewer

Updated Jul 29, 2026
Python

Scindices / VicFisher--DiffPhore

Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping

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 method-diffusion

Updated Jun 5, 2026
Python

Scindices / SeonghwanSeo--PharmacoNet

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 / psi4--psi4

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

status-active lang-python lang-cpp interface-cli entity-small-molecule interface-api status-published status-packaged-conda scope-focused role-toolkit domain-computational-chemistry task-quantum-chemistry method-quantum

Updated Jul 24, 2026
C++

Scindices / molssi-seamm--molsystem

Molsystem provides a general class for handling molecular and periodic systems

status-active role-library lang-python domain-cheminformatics method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi scope-focused method-physics domain-molecular-simulation task-system-model entity-crystal

Updated Jun 30, 2026
Python

Scindices / MolSSI--QCEngine

Quantum chemistry program executor and IO standardizer (QCSchema).

status-active lang-python interface-cli role-framework task-workflow entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-computational-chemistry task-quantum-chemistry method-quantum

Updated Jul 28, 2026
Python

Scindices / uibcdf--OpenPharmacophore

An open library to work with pharmacophores.

role-library lang-python status-archived domain-cheminformatics method-chemoinformatics entity-protein entity-small-molecule interface-api status-published scope-focused domain-drug-discovery entity-complex task-pharmacophore ecosystem-molsys

Updated Jul 6, 2023
Python

Scindices / coleygroup--shepherd

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 / AngelRuizMoreno--ConcensusPharmacophore

Consensus pharmacophore for Drug Design

status-active role-library lang-python domain-cheminformatics method-chemoinformatics entity-protein entity-small-molecule interface-api interface-jupyter status-published scope-focused domain-drug-discovery ecosystem-rdkit task-pharmacophore

Updated Aug 22, 2025
Jupyter Notebook

Scindices / aspuru-guzik-group--selfies

Robust representation of semantically constrained graphs, in particular for molecules in chemistry

entity-graph status-active role-library lang-python domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery task-featurization task-molecular-generation

Updated May 17, 2025
Python

Scindices / forlilab--Meeko

Interface for AutoDock, molecule parameterization

Updated Jul 10, 2026
Python

Add this topic to your repo

To associate your repository with the entity-small-molecule topic, visit your repo's landing page and select "manage topics."