zhangdachuanfoodies

atlas

ATLAS - Three commands to start analyzing your metagenome data

AutoDock-Vina

AutoDock Vina

Aviator

bidd-molmap

MolMap: An Efficient Convolutional Neural Network Based Molecular Deep Learning Tool

CGRtools

CGRs, molecules and reactions manipulation

chemprop

Message Passing Neural Networks for Molecule Property Prediction

CIMtools

DLKcat

Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction

dMaSIF

dockstore

Our VM/Docker sharing infrastructure and management component

EnzyDock

EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes

EnzyHTP

Forum-DiseasesChem

A Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases.

MAHOMES

Metal Activity Heuristic of Metalloprotein and Enzymatic Sites (MAHOMES) - Predicts if a protein bound metal ion is enzymatic or non-enzymatic

mdfptools

mindsdb

In-Database Machine Learning

NPS-generation

OPERA

Free and open-source application (command line and GUI) providing QSAR models predictions as well as applicability domain and accuracy assessment for physicochemical properties, environmental fate and toxicological endpoints. ==================>Download the latest compiled version from the "releases" tab and run the executable installer.

Prediction_of_adaptor_proteins_using_PSSM_profiles_and_Recurrent_Neural_Networks.

This study opens the path for Recurrent Neural Network (RNN) and Position-Specific Scoring Matrix (PSSM) structures to be employed in computational biology and bioinformatics. The research approach we promote for is applicable to scientists who aim to improve the prediction results of protein function prediction problems.

PrimeKG

Precision Medicine Knowledge Graph (PrimeKG)

pssmpro

A python tool for numerically encoding protein sequences based on PSSM profile

pyADA

A cheminformatics package to perform Applicability Domain of molecular fingerprints based in similarity calculation.

PyPLIF-HIPPOS

HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS

RetroBioCat

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).

rxnmapper

RXNMapper: Unsupervised attention-guided atom-mapping. Code complementing our Science Advances publication on "Extraction of organic chemistry grammar from unsupervised learning of chemical reactions" (https://advances.sciencemag.org/content/7/15/eabe4166).

selfies

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

teachopencadd

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

toxsmi

Toxicity prediction models

VirtualScreening

The repository contains supplementary files to our study where a consensus screening approach by using different types of machine learning models (proteochemometric models, conformal prediction models, and QSAR models), followed by structure-based virtual screening of preselected hits using the structural models for hepatic OATPs was performed.