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PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/3527603948.ch10openalex-snapshot

Proteochemometrics: A Tool for Modeling the Molecular Interaction Space

inferredcites →https://doi.org/10.1002/9780470122921.ch2openalex-snapshot

Prediction of the Secondary Structure of Proteins from their Amino Acid Sequence

inferredcites →https://doi.org/10.1002/bip.360270308openalex-snapshot

Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities

inferredcites →https://doi.org/10.1002/cem.1321openalex-snapshot

Prediction of aqueous solubility of druglike organic compounds using partial least squares, back‐propagation network and support vector machine

inferredcites →https://doi.org/10.1002/cem.1416openalex-snapshot

Computer‐aided prediction of toxicity with substructure pattern and random forest

inferredcites →https://doi.org/10.1002/prot.1035openalex-snapshot

Prediction of protein cellular attributes using pseudo‐amino acid composition

inferredcites →https://doi.org/10.1002/qsar.200630094openalex-snapshot

In Silico ADME Modeling 3: Computational Models to Predict Human Intestinal Absorption Using Sphere Exclusion and kNN QSAR Methods

inferredcites →https://doi.org/10.1006/bbrc.2000.3815openalex-snapshot

Prediction of Protein Subcellular Locations by Incorporating Quasi-Sequence-Order Effect

inferredcites →https://doi.org/10.1007/s00894-002-0101-1openalex-snapshot

ADME evaluation in drug discovery

inferredcites →https://doi.org/10.1016/0022-5193(67)90004-5openalex-snapshot

On the average hydrophobicity of proteins and the relation between it and protein structure

inferredcites →https://doi.org/10.1016/0022-5193(82)90191-6openalex-snapshot

The structural dependence of amino acid hydrophobicity parameters

inferredcites →https://doi.org/10.1016/j.ab.2007.10.012openalex-snapshot

PseAAC: A flexible web server for generating various kinds of protein pseudo amino acid composition

inferredcites →https://doi.org/10.1016/j.aca.2011.02.010openalex-snapshot

In silico classification of human maximum recommended daily dose based on modified random forest and substructure fingerprint

inferredcites →https://doi.org/10.1016/j.aca.2012.09.021openalex-snapshot

Large-scale prediction of drug–target interactions using protein sequences and drug topological structures

inferredcites →https://doi.org/10.1016/j.bbrc.2004.06.073openalex-snapshot

Prediction of protein subcellular locations by GO–FunD–PseAA predictor

inferredcites →https://doi.org/10.1016/j.biochi.2012.03.022openalex-snapshot

Using core hydrophobicity to identify phosphorylation sites of human G protein-coupled receptors

inferredcites →https://doi.org/10.1016/j.ddtec.2006.12.008openalex-snapshot

In silico target fishing: Predicting biological targets from chemical structure

inferredcites →https://doi.org/10.1016/j.drudis.2006.08.013openalex-snapshot

Chemogenomics: structuring the drug discovery process to gene families

inferredcites →https://doi.org/10.1016/j.drudis.2006.10.005openalex-snapshot

Similarity-based virtual screening using 2D fingerprints

inferredcites →https://doi.org/10.1016/j.febslet.2008.02.024openalex-snapshot

Large‐scale prediction of drug–target relationships

inferredcites →https://doi.org/10.1016/s0026-895x(24)12106-2openalex-snapshot

Proteochemometrics Modeling of the Interaction of Amine G-Protein Coupled Receptors with a Diverse Set of Ligands

inferredcites →https://doi.org/10.1021/ci00046a002openalex-snapshot

Atom pairs as molecular features in structure-activity studies: definition and applications

inferredcites →https://doi.org/10.1021/ci00054a008openalex-snapshot

Topological torsion: a new molecular descriptor for SAR applications. Comparison with other descriptors

inferredcites →https://doi.org/10.1021/ci025569topenalex-snapshot

Similarity Metrics for Ligands Reflecting the Similarity of the Target Proteins

inferredcites →https://doi.org/10.1021/ci025584yopenalex-snapshot

The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics

inferredcites →https://doi.org/10.1021/ci034160gopenalex-snapshot

Random Forest: A Classification and Regression Tool for Compound Classification and QSAR Modeling

inferredcites →https://doi.org/10.1021/ci034280oopenalex-snapshot

Study of the Quantitative Structure-Mobility Relationship of Carboxylic Acids in Capillary Electrophoresis Based on Support Vector Machines

inferredcites →https://doi.org/10.1021/ci049778kopenalex-snapshot

Pharmacophore Identification, in Silico Screening, and Virtual Library Design for Inhibitors of the Human Factor Xa

inferredcites →https://doi.org/10.1021/ci100050topenalex-snapshot

Extended-Connectivity Fingerprints

inferredcites →https://doi.org/10.1021/ci100104jopenalex-snapshot

Estimation of ADME Properties with Substructure Pattern Recognition

inferredcites →https://doi.org/10.1021/ci600343xopenalex-snapshot

ADME Evaluation in Drug Discovery. 7. Prediction of Oral Absorption by Correlation and Classification

inferredcites →https://doi.org/10.1021/ci980140gopenalex-snapshot

Binary Quantitative Structure−Activity Relationship (QSAR) Analysis of Estrogen Receptor Ligands

inferredcites →https://doi.org/10.1021/jm020945mopenalex-snapshot

QSAR and Proteo-chemometric Analysis of the Interaction of a Series of Organic Compounds with Melanocortin Receptor Subtypes

inferredcites →https://doi.org/10.1021/jm990472sopenalex-snapshot

2D QSAR Modeling and Preliminary Database Searching for Dopamine Transporter Inhibitors Using Genetic Algorithm Variable Selection of Molconn Z Descriptors

inferredcites →https://doi.org/10.1023/a:1007091128394openalex-snapshot

Prediction of Membrane Protein Types Based on the Hydrophobic Index of Amino Acids

inferredcites →https://doi.org/10.1023/a:1010933404324openalex-snapshot

Random Forests

inferredcites →https://doi.org/10.1023/a:1010967008838openalex-snapshot

Accurate Prediction of Protein Secondary Structural Content

inferredcites →https://doi.org/10.1038/nature08506openalex-snapshot

Predicting new molecular targets for known drugs

inferredcites →https://doi.org/10.1038/nature11159openalex-snapshot

Large-scale prediction and testing of drug activity on side-effect targets

inferredcites →https://doi.org/10.1038/nbt1284openalex-snapshot

Relating protein pharmacology by ligand chemistry

inferredcites →https://doi.org/10.1038/ng1109openalex-snapshot

Bioinformatics in the post-sequence era

inferredcites →https://doi.org/10.1038/nprot.2007.494openalex-snapshot

Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms

inferredcites →https://doi.org/10.1038/nrd1032openalex-snapshot

ADMET in silico modelling: towards prediction paradise?

inferredcites →https://doi.org/10.1038/nrd1468openalex-snapshot

Drug repositioning: identifying and developing new uses for existing drugs

inferredcites →https://doi.org/10.1038/nrd3478openalex-snapshot

Trends in the exploitation of novel drug targets

inferredcites →https://doi.org/10.1038/nrg1317openalex-snapshot

Chemogenomics: an emerging strategy for rapid target and drug discovery

inferredcites →https://doi.org/10.1073/pnas.0607879104openalex-snapshot

Predicting protein–protein interactions based only on sequences information

inferredcites →https://doi.org/10.1073/pnas.92.19.8700openalex-snapshot

Prediction of protein folding class using global description of amino acid sequence.

inferredcites →https://doi.org/10.1074/jbc.m204161200openalex-snapshot

Using Functional Domain Composition and Support Vector Machines for Prediction of Protein Subcellular Location

inferredcites →https://doi.org/10.1074/jbc.m401932200openalex-snapshot

Classification of Nuclear Receptors Based on Amino Acid Composition and Dipeptide Composition

inferredcites →https://doi.org/10.1093/bioinformatics/17.5.455openalex-snapshot

Predicting protein–protein interactions from primary structure

inferredcites →https://doi.org/10.1093/bioinformatics/bth466openalex-snapshot

Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes

inferredcites →https://doi.org/10.1093/bioinformatics/bti703openalex-snapshot

Improved approach for proteochemometrics modeling: application to organic compound—amine G protein-coupled receptor interactions

inferredcites →https://doi.org/10.1093/bioinformatics/btn162openalex-snapshot

Prediction of drug–target interaction networks from the integration of chemical and genomic spaces

inferredcites →https://doi.org/10.1093/bioinformatics/btn397openalex-snapshot

BioJava: an open-source framework for bioinformatics

inferredcites →https://doi.org/10.1093/bioinformatics/btq176openalex-snapshot

Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework

inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/27.1.368openalex-snapshot

AAindex: Amino Acid Index Database

inferredcites →https://doi.org/10.1093/nar/29.1.242openalex-snapshot

BIND--The Biomolecular Interaction Network Database

inferredcites →https://doi.org/10.1093/nar/30.1.303openalex-snapshot

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

inferredcites →https://doi.org/10.1093/nar/30.1.412openalex-snapshot

TTD: Therapeutic Target Database

inferredcites →https://doi.org/10.1093/nar/gkg056openalex-snapshot

BIND: the Biomolecular Interaction Network Database

inferredcites →https://doi.org/10.1093/nar/gkg600openalex-snapshot

SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence

inferredcites →https://doi.org/10.1093/nar/gkl305openalex-snapshot

PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

inferredcites →https://doi.org/10.1093/nar/gkl999openalex-snapshot

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

inferredcites →https://doi.org/10.1093/nar/gkm862openalex-snapshot

SuperTarget and Matador: resources for exploring drug-target relationships

inferredcites →https://doi.org/10.1093/nar/gkm958openalex-snapshot

DrugBank: a knowledgebase for drugs, drug actions and drug targets

inferredcites →https://doi.org/10.1093/nar/gkn760openalex-snapshot

STRING 8--a global view on proteins and their functional interactions in 630 organisms

inferredcites →https://doi.org/10.1093/nar/gkn892openalex-snapshot

Human Protein Reference Database--2009 update

inferredcites →https://doi.org/10.1093/nar/gkr777openalex-snapshot

ChEMBL: a large-scale bioactivity database for drug discovery

inferredcites →https://doi.org/10.1126/science.1158140openalex-snapshot

Drug Target Identification Using Side-Effect Similarity

inferredcites →https://doi.org/10.1186/1471-2105-9-181openalex-snapshot

Proteochemometric modeling of HIV protease susceptibility

inferredcites →https://doi.org/10.1186/1752-153x-2-24openalex-snapshot

Cinfony – combining Open Source cheminformatics toolkits behind a common interface

inferredcites →https://doi.org/10.1186/1758-2946-3-1openalex-snapshot

CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

inferredcites →https://doi.org/10.1186/1758-2946-3-33openalex-snapshot

Open Babel: An open chemical toolbox

inferredcites →https://doi.org/10.1186/1758-2946-3-s1-o14openalex-snapshot

De novodesign of molecular wires with optimal properties for solar energy conversion

inferredcites →https://doi.org/10.1371/journal.pone.0009603openalex-snapshot

Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features

inferredcites →https://doi.org/10.1371/journal.pone.0027518openalex-snapshot

Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide Preclinical Development

inferredcites →https://doi.org/10.1371/journal.pone.0037608openalex-snapshot

A Systematic Prediction of Multiple Drug-Target Interactions from Chemical, Genomic, and Pharmacological Data

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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TargetNet: a web service for predicting potential drug–target interaction profiling via multi-target SAR models

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Development and validation of consensus machine learning-based models for the prediction of novel small molecules as potential anti-tubercular agents

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Machine learning-enabled predictive modeling to precisely identify the antimicrobial peptides

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Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches

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Targeting GPCRs Via Multi-Platform Arrays and AI

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Introduction to python

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The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein–Ligand and Protein–Protein Interactions Landscapes for Drug Discovery

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ENNAACT is a novel tool which employs neural networks for anticancer activity classification for therapeutic peptides

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In silico toxicity prediction of chemicals from EPA toxicity database by kernel fusion-based support vector machines

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Automating data analysis for two-dimensional gas chromatography/time-of-flight mass spectrometry non‐targeted analysis of comparative samples

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A comprehensive review of feature based methods for drug target interaction prediction

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ChemSAR: an online pipelining platform for molecular SAR modeling

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Additional file 1 of PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling

inferred← citeshttps://doi.org/10.6084/m9.figshare.19919443openalex-snapshot

Additional file 6 of PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling

inferred← citeshttps://doi.org/10.6084/m9.figshare.19919446openalex-snapshot

Additional file 7 of PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling

inferred← citeshttps://doi.org/10.6084/m9.figshare.26584359openalex-snapshot

Additional file 1 of In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences

inferred← citeshttps://doi.org/10.6084/m9.figshare.26584362openalex-snapshot

Additional file 2 of In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences

inferred← citeshttps://doi.org/10.6084/m9.figshare.26584365openalex-snapshot

Additional file 3 of In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences

inferred← citeshttps://doi.org/10.6084/m9.figshare.26584368openalex-snapshot

Additional file 4 of In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences

inferred← citeshttps://doi.org/10.6084/m9.figshare.26584371openalex-snapshot

Additional file 5 of In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences

inferred← citeshttps://doi.org/10.6084/m9.figshare.26607286openalex-snapshot

Additional file 1 of PyL3dMD: Python LAMMPS 3D molecular descriptors package

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