virtual-screening

There are 7 repositories under virtual-screening topic.

kexinhuang12345 / DeepPurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
drug-repurposing deep-learning drug-target-interactions toolkit covid19 virtual-screening drug-discovery ppi ddi dti-prediction drug-property-prediction protein-function-prediction repurposing-drugs qsar side-effects drug-drug-interaction protein-protein-interaction drug-target-interaction bioinformatics
Language:Jupyter Notebook 939
p2rank
rdk / p2rank
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
bioinformatics machine-learning protein-structure pdb binding-sites proteins ligand protein-surface structural-bioinformatics protein-ligand-interactions java random-forest mmcif pymol groovy protein-ligand-docking molecular-structures drug-discovery virtual-screening p2rank
Language:Groovy 234
coleygroup / molpal
active learning for accelerated high-throughput virtual screening
active-learning chemistry virtual-screening
Language:Jupyter Notebook 158
aamini / chemprop
Fast and scalable uncertainty quantification for neural molecular property prediction, accelerated optimization, and guided virtual screening.
drug-discovery uncertainty molecule evidential-deep-learning chemistry active-learning bayesian-optimization virtual-screening neural-network
Language:Python 107
jamesgleave / DD_protocol
Official repository for the Deep Docking protocol
deep-learning docking drug-discovery virtual-screening
Language:Python 91
coleygroup / pyscreener
pythonic interface to virtual screening software
virtual-screening computational-biology molecular-docking distributed-computing ray
Language:Python 83
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
SteshinSS / lohi_splitter
Lo-Hi Splitter for Modern Splits of Molecular Datasets
drug drug-design drug-discovery molecular-generation virtual-screening
Language:Jupyter Notebook 51
CBDD / rDock
rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies.
docking drug-discovery virtual-screening
Language:C++ 47
SeonghwanSeo / PharmacoNet
Official Github for "PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modeling" (NeurIPS 2023 Workshop)
deep-learning drug-discovery instance-segmentation machine-learning pharmacophore-modelling virtual-screening pharmacophore
Language:Python 35
denoptim-project / DENOPTIM
DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind.
molecular-design molecular-modeling computational-chemistry de-novo-design virtual-screening genetic-algorithm combinatorial
Language:Java 33
RyanZR / labodock
LABODOCK: A Colab-Based Molecular Docking Tools
autodock-vina cheminformatics drug-design google-colab molecular-docking plip virtual-screening
Language:Jupyter Notebook 32
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 26
rasbt / screenlamp
screenlamp is a Python toolkit for hypothesis-driven virtual screening
virtual-screening drug-discovery python ligand-screening computational-biology bioinformatics docking computational-chemistry pharmacometrics
Language:Python 22
jRicciL / ML-ensemble-docking
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning
machine-learning protein-structure drug-discovery virtual-screening docking
Language:Jupyter Notebook 21
YanjunLi-CS / dyscore
Open source code for DyScore
de-novo-drug-design drug-discovery protein-ligand-interactions scoring-functions virtual-screening
Language:Python 20
automated-qsar-framework
LabMolUFG / automated-qsar-framework
Automated framework for the curation of chemogenomics data and to develop QSAR models for virtual screening using the open-source KNIME software
cheminformatics qsar drug-discovery virtual-screening machine-learning knime
18
taneishi / DeepLBVS
Ligand-based Virtual Screening using Deep Learning
ligand-based virtual-screening deep-learning
Language:Python 16
MoleculeTransformers / smiles-featurizers
Extract Molecular SMILES embeddings from language models pre-trained with various objectives architectures.
embeddings pytorch smiles bert sentence-embeddings sentence-transformers simcse bart fingerprints bart-decoder bart-encoder dense-vectors moleculenet virtual-screening virtual-screening-studies
Language:Python 15
tsudalab / ACP4
AutoCorrelation of Pharmacophore Features
autocorrelation binding-site ocaml-program pharmacophore virtual-screening ligand ligand-binding-site
Language:OCaml 15
mcsorkun / V2DB
V2DB (Virtual 2D Materials Database): the code for generating and predicting the novel 2D materials by virtual screening.
2d-materials dataset material-science machine-learning virtual-screening
Language:Python 12
DockM8
DrugBud-Suite / DockM8
All in one Structure-Based Vitual 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 10
XiaohuaZhangLLNL / conveyorlc
A pipeline to do virtual screening
docking-calculation mmgbsa virtual-screening
Language:C++ 10
filipsPL / tox21_dataset
Datasets used in the tox21 challenge
challenge compound dataset fingerprints machine-learning prioritization tox21 toxicity virtual-screening
9
psa-lab / siteinterlock
A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics
protein-ligand-docking bioinformatics biological-data-analysis protein-structure virtual-screening python computational-biology
Language:Python 9
quantaosun / Zinc-Million
Open-Sourced. Millions of small molecules will be downloaded from the ZINC database in 3D SDF file format, with one click, to get ready for a large scale virtual screening for certain protein target.
chembl schrodinger virtual-screening
Language:Jupyter Notebook 9
alvesvm / sars-cov-mpro
QSAR models and putative agents identified against SARS-CoV-2
sars-cov sars-cov-2 covid-19 covid19 qsar machine-learning virtual-screening drugbank hits drugs mpro
Language:Jupyter Notebook 8
gitter-lab / pria_lifechem
Virtual screening on PriA-SSB and RMI-FANCM with the LifeChem library
virtual-screening neural-network biochemistry
Language:Jupyter Notebook 8
docktgrid
gmmsb-lncc / docktgrid
Create customized voxel representations of protein-ligand complexes using GPU.
deep-learning molecular-docking scoring-functions binding-affinity virtual-screening voxel-grid
Language:Python 8
SeonghwanSeo / OpenPharmaco
Open-source protein-based pharmacophore modeling software
deep-learning drug-discovery machine-learning pharmacophore-modelling protein-based-pharmacophore-modelling virtual-screening
Language:Python 7
dehaenw / RiFF
Reaction-informed Fusion of Fragments (RiFF
cheminformatics virtual-screening
Language:Python 6
gitter-lab / pria-ams-enamine
Virtual screening on PriA-SSB with the AMS and Enamine REAL libraries
virtual-screening machine-learning biochemistry
Language:Jupyter Notebook 6
filipsPL / fingernat-ml
Data accompanying the manuscript on SIFts- and ML-based methods in Virtual Screening for RNA binding ligands.
benchmark rna rna-ligand virtual-screening
5
jwxia2014 / MUBD-HDACs
Maximal Unbiased Benchmarking Datasets for Histone Deacetylases and Sirtuin Family
virtual-screening computer-aided-drug-design benchmark hdac
5
taoshen99 / MUBDsyn
The official repository for the CBM paper "Deep Reinforcement Learning Enables Better Bias Control in Benchmark for Virtual Screening".
benchmark-datasets machine-learning synthetic-data virtual-screening generative-model reinforcement-learning
Language:Python 5
2040FBDBIC
UAMCAntwerpen / 2040FBDBIC
This repository contains all the course materials that are used in the "Chemo-informatics and computational drug design" course teaches at the University of Antwerp (Belgium)
cheminformatics computational-chemistry course drug-design drug-discovery glide machine-learning maestro molecular-dynamics molecular-dynamics-simulation molecular-mechanics pharmacophore-modelling python rdkit schrodinger virtual-machine virtual-screening drug-receptor-interaction universiteit-antwerpen
Language:Jupyter Notebook 5

virtual-screening

kexinhuang12345 / DeepPurpose

rdk / p2rank

coleygroup / molpal

aamini / chemprop

jamesgleave / DD_protocol

coleygroup / pyscreener

rxdock / rxdock

SteshinSS / lohi_splitter

CBDD / rDock

SeonghwanSeo / PharmacoNet

denoptim-project / DENOPTIM

RyanZR / labodock

radifar / PyPLIF-HIPPOS

rasbt / screenlamp

jRicciL / ML-ensemble-docking

YanjunLi-CS / dyscore

LabMolUFG / automated-qsar-framework

taneishi / DeepLBVS

MoleculeTransformers / smiles-featurizers

tsudalab / ACP4

mcsorkun / V2DB

DrugBud-Suite / DockM8

XiaohuaZhangLLNL / conveyorlc

filipsPL / tox21_dataset

psa-lab / siteinterlock

quantaosun / Zinc-Million

alvesvm / sars-cov-mpro

gitter-lab / pria_lifechem

gmmsb-lncc / docktgrid

SeonghwanSeo / OpenPharmaco

dehaenw / RiFF

gitter-lab / pria-ams-enamine

filipsPL / fingernat-ml

jwxia2014 / MUBD-HDACs

taoshen99 / MUBDsyn

UAMCAntwerpen / 2040FBDBIC