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 1082
p2rank
rdk / p2rank
P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
bioinformatics machine-learning protein-structure pdb binding-sites proteins structural-bioinformatics java mmcif pymol groovy protein-ligand-docking molecular-structures drug-discovery virtual-screening p2rank chimerax protein-ligand-interactions docking ligand
Language:Groovy 344
coleygroup / molpal
active learning for accelerated high-throughput virtual screening
active-learning chemistry virtual-screening
Language:Jupyter Notebook 180
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 124
jamesgleave / DD_protocol
Official repository for the Deep Docking protocol
deep-learning docking drug-discovery virtual-screening
Language:Python 121
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
SeonghwanSeo / PharmacoNet
Official Github for "PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening" (Chemical Science)
deep-learning drug-discovery instance-segmentation machine-learning pharmacophore-modelling virtual-screening pharmacophore
Language:Python 66
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++ 54
DrugBud-Suite / CADD_Vault
chemistry cheminformatics chemoinformatics computational-chemistry computational-biology computational-physics compchem drug-discovery drugs drug-repurposing drug-design protein-ligand-interactions virtual-screening molecular-dynamics molecular-modeling molecular-simulation sbvs
Language:HTML 54
SteshinSS / lohi_splitter
Lo-Hi Splitter for Modern Splits of Molecular Datasets
drug drug-design drug-discovery molecular-generation virtual-screening
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 49
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 47
denoptim-project / DENOPTIM
DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind.
combinatorial computational-chemistry de-novo-design genetic-algorithm molecular-design molecular-modeling virtual-screening
Language:Java 37
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 29
VicFisher / DiffPhore
Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping
conformation-generation geometric-deep-learning metalloenyzme pharmacophore target-fishing virtual-screening
Language:Python 29
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 23
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 23
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 23
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
20
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 20
YanjunLi-CS / dyscore
Open source code for DyScore
de-novo-drug-design drug-discovery protein-ligand-interactions scoring-functions virtual-screening
Language:Python 20
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 17
taneishi / DeepLBVS
Ligand-based Virtual Screening using Deep Learning
deep-learning ligand-based virtual-screening
Language:Python 16
tsudalab / ACP4
AutoCorrelation of Pharmacophore Features
autocorrelation binding-site ocaml-program pharmacophore virtual-screening ligand ligand-binding-site
Language:OCaml 15
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 11
filipsPL / tox21_dataset
Datasets used in the tox21 challenge
toxicity compound dataset prioritization virtual-screening fingerprints machine-learning tox21 challenge
10
XiaohuaZhangLLNL / conveyorlc
A pipeline to do virtual screening
docking-calculation mmgbsa virtual-screening
Language:C++ 10
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 9
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
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
bioinformatics biological-data-analysis computational-biology protein-ligand-docking protein-structure python virtual-screening
Language:Python 9
dehaenw / RiFF
Reaction-informed Fusion of Fragments (RiFF
cheminformatics virtual-screening
Language:Python 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
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 8
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 drug-receptor-interaction glide machine-learning maestro molecular-dynamics molecular-dynamics-simulation molecular-mechanics pharmacophore-modelling python rdkit schrodinger universiteit-antwerpen virtual-machine virtual-screening
Language:Jupyter Notebook 7
PDB-CAT
URV-cheminformatics / PDB-CAT
PDB-CAT aims to automatically categorize the mmCIF PDB structures based on the type of interaction between atoms in the protein and the ligand, and checking for any mutations in the sequence.
drug-discovery virtual-screening
Language:Jupyter Notebook 7