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Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME
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1 of the 67 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-11): 10.1128/mcb.00935-12 (notice 2018-07-30).
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists
inferredcites →https://doi.org/10.1002/1097-0282(2002)61:2<127::aid-bip10076>3.0.co;2-nopenalex-snapshot
The binding database: Overview and user's guide
inferredcites →https://doi.org/10.1002/3527603743.ch9openalex-snapshot
WOMBAT: World of Molecular Bioactivity
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Similarity Searching in Databases of Chemical Structures
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The bioinformatics of molecular recognition
inferredcites →https://doi.org/10.1002/prot.20277openalex-snapshot
Enzyme classification by ligand binding
inferredcites →https://doi.org/10.1002/qsar.200330831openalex-snapshot
Approaches to Measure Chemical Similarity – a Review
inferredcites →https://doi.org/10.1007/0-306-46857-3_13openalex-snapshot
Similarity and Dissimilarity: A Medicinal Chemist’s View
inferredcites →https://doi.org/10.1007/978-3-540-78246-9_38openalex-snapshot
KNIME: The Konstanz Information Miner
inferredcites →https://doi.org/10.1007/s10822-012-9577-7openalex-snapshot
Scientific workflow systems: Pipeline Pilot and KNIME
inferredcites →https://doi.org/10.1016/0014-2999(96)00402-5openalex-snapshot
Cyclobenzaprine, a centrally acting muscle relaxant, acts on descending serotonergic systems
inferredcites →https://doi.org/10.1016/j.drudis.2012.05.016openalex-snapshot
Open PHACTS: semantic interoperability for drug discovery
inferredcites →https://doi.org/10.1016/s0022-2836(77)80200-3openalex-snapshot
The protein data bank: A computer-based archival file for macromolecular structures
inferredcites →https://doi.org/10.1016/s1053-8119(03)00185-xopenalex-snapshot
The LONI Pipeline Processing Environment
inferredcites →https://doi.org/10.1016/s1353-8020(99)00042-5openalex-snapshot
Acute dystonia in a young schizophrenic patient associated with ingestion of a cloperastine containing cough syrup
inferredcites →https://doi.org/10.1016/s1574-1400(08)00012-1openalex-snapshot
PubChem: Integrated Platform of Small Molecules and Biological Activities
inferredcites →https://doi.org/10.1021/ci00007a012openalex-snapshot
Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited
inferredcites →https://doi.org/10.1021/ci020017wopenalex-snapshot
The Maximum Common Substructure as a Molecular Depiction in a Supervised Classification Context: Experiments in Quantitative Structure/Biodegradability Relationships
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/ci050011hopenalex-snapshot
Database Clustering with a Combination of Fingerprint and Maximum Common Substructure Methods
inferredcites →https://doi.org/10.1021/ci060003gopenalex-snapshot
Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases
inferredcites →https://doi.org/10.1021/ci1003174openalex-snapshot
ReverseScreen3D: A Structure-Based Ligand Matching Method To Identify Protein Targets
inferredcites →https://doi.org/10.1021/ci300601qopenalex-snapshot
Enhancing Molecular Shape Comparison by Weighted Gaussian Functions
inferredcites →https://doi.org/10.1021/ci400466ropenalex-snapshot
Heterogeneous Classifier Fusion for Ligand-Based Virtual Screening: Or, How Decision Making by Committee Can Be a Good Thing
inferredcites →https://doi.org/10.1021/ci9902696openalex-snapshot
JChem: Java Applets and Modules Supporting Chemical Database Handling from Web Browsers
inferredcites →https://doi.org/10.1021/ja025304vopenalex-snapshot
Pipeline Pilot 2.1 By Scitegic, 9665 Chesapeake Drive, Suite 401, San Diego, CA 92123-1365. www.scitegic.com. See Web Site for Pricing Information
inferredcites →https://doi.org/10.1021/jm020155copenalex-snapshot
Do Structurally Similar Molecules Have Similar Biological Activity?
inferredcites →https://doi.org/10.1021/jm030242kopenalex-snapshot
Shape Signatures: A New Approach to Computer-Aided Ligand- and Receptor-Based Drug Design
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm0600545openalex-snapshot
Inhibition ofPlasmodiumfalciparumFatty Acid Biosynthesis: Evaluation of FabG, FabZ, and FabI as Drug Targets for Flavonoids
inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot
Comparison of Shape-Matching and Docking as Virtual Screening Tools
inferredcites →https://doi.org/10.1021/jm401411zopenalex-snapshot
Molecular Similarity in Medicinal Chemistry
inferredcites →https://doi.org/10.1023/a:1016387816342openalex-snapshot
Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases
inferredcites →https://doi.org/10.1023/a:1027221424359openalex-snapshot
Similarity and Dissimilarity: A Medicinal Chemist's View
inferredcites →https://doi.org/10.1038/nature08506openalex-snapshot
Predicting new molecular targets for known drugs
inferredcites →https://doi.org/10.1038/nbt1284openalex-snapshot
Relating protein pharmacology by ligand chemistry
inferredcites →https://doi.org/10.1038/nm.3618openalex-snapshot
Micropillar arrays as a high-throughput screening platform for therapeutics in multiple sclerosis
inferredcites →https://doi.org/10.1038/sj.bjp.0701079openalex-snapshot
High affinity of sigma1‐binding sites for sterol isomerization inhibitors: evidence for a pharmacological relationship with the yeast sterol C8–C7 isomerase
inferredcites →https://doi.org/10.1038/sj.bjp.0705605openalex-snapshot
Antitussive activity of sigma‐1 receptor agonists in the guinea‐pig
inferredcites →https://doi.org/10.1039/b409813gopenalex-snapshot
Molecular similarity: a key technique in molecular informatics
inferredcites →https://doi.org/10.1073/pnas.1204524109openalex-snapshot
Identifying mechanism-of-action targets for drugs and probes
inferredcites →https://doi.org/10.1093/bioinformatics/18.1.130openalex-snapshot
The Binding Database: data management and interface design
inferredcites →https://doi.org/10.1093/bioinformatics/btn186openalex-snapshot
A maximum common substructure-based algorithm for searching and predicting drug-like compounds
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/28.1.27openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/gki070openalex-snapshot
The Universal Protein Resource (UniProt)
inferredcites →https://doi.org/10.1093/nar/gkl320openalex-snapshot
Taverna: a tool for building and running workflows of services
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/gkt1031openalex-snapshot
The ChEMBL bioactivity database: an update
inferredcites →https://doi.org/10.1093/nar/gni148openalex-snapshot
A highly sensitive selection method for directed evolution of homing endonucleases
inferredcites →https://doi.org/10.1101/gr.4086505openalex-snapshot
Galaxy: A platform for interactive large-scale genome analysis
inferredcites →https://doi.org/10.1107/s0907444905029604openalex-snapshot
Non-steroidal anti-inflammatory drugs as potent inhibitors of phospholipase A2: structure of the complex of phospholipase A2with niflumic acid at 2.5 Å resolution
inferredcites →https://doi.org/10.1107/s0907444906003660openalex-snapshot
Specific binding of non-steroidal anti-inflammatory drugs (NSAIDs) to phospholipase A2: structure of the complex formed between phospholipase A2and diclofenac at 2.7 Å resolution
inferredcites →https://doi.org/10.1109/ssdm.2004.1311178openalex-snapshot
16th International Conference on Scientific and Statistical Database Management
inferredcites →https://doi.org/10.1111/j.1469-8749.2011.04105.xopenalex-snapshot
Cloperastine‐based cough syrup and acute dystonic reactions
inferredcites →https://doi.org/10.1111/j.1747-0285.2006.00384.xopenalex-snapshot
PHASE: A Novel Approach to Pharmacophore Modeling and 3D Database Searching
inferredcites →https://doi.org/10.1128/mcb.00935-12openalex-snapshot
RETRACTED ARTICLE: The Breast Cancer Susceptibility Gene Product Fibroblast Growth Factor Receptor 2 Serves as a Scaffold for Regulation of NF-κB Signaling
inferredcites →https://doi.org/10.1146/annurev-pharmtox-010611-134520openalex-snapshot
Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action
inferredcites →https://doi.org/10.1177/107385840000600408openalex-snapshot
The Multiplicity of Serotonin Receptors: Uselessly Diverse Molecules or an Embarrassment of Riches?
inferredcites →https://doi.org/10.1186/gb-2010-11-8-r86openalex-snapshot
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
inferredcites →https://doi.org/10.2147/tcrm.s16643openalex-snapshot
Pharmacological and clinical overview of cloperastine in treatment of cough
inferredcites →https://doi.org/10.2174/1386207013330670openalex-snapshot
BindingDB: A Web-Accessible Molecular Recognition Database
inferredcites →https://doi.org/10.2174/138620707780126705openalex-snapshot
Target Specific Compound Identification Using a Support Vector Machine
inferredcites →https://doi.org/10.2174/156802612804547362openalex-snapshot
Target Prediction of Small Molecules with Information of Key Molecular Interactions
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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An automated curation procedure for addressing chemical errors and inconsistencies in public datasets used in QSAR modelling
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PTS: a pharmaceutical target seeker
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BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology
inferred← citeshttps://doi.org/10.1109/access.2025.3583338openalex-snapshot
Binding Affinity Prediction for Pancreatic Ductal Adenocarcinoma Using Drug-Target Descriptors and Artificial Intelligence
inferred← citeshttps://doi.org/10.1124/mol.117.110940openalex-snapshot
The Bioactive Protein-Ligand Conformation of GluN2C-Selective Positive Allosteric Modulators Bound to the NMDA Receptor
inferred← citeshttps://doi.org/10.1186/s13321-017-0198-yopenalex-snapshot
Analysis of drug–endogenous human metabolite similarities in terms of their maximum common substructures
inferred← citeshttps://doi.org/10.1186/s13321-017-0256-5openalex-snapshot
An automated framework for QSAR model building
inferred← citeshttps://doi.org/10.1186/s13321-020-0408-xopenalex-snapshot
Towards reproducible computational drug discovery
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Unrecognised Outbreak: Human parainfluenza virus infections in a pediatric oncology unit. A new diagnostic PCR and virus monitoring system may allow early detection of future outbreaks
inferred← citeshttps://doi.org/10.2174/0929867326666190409141016openalex-snapshot
Ligand- and Structure-Based Drug Design and Optimization using KNIME
inferred← citeshttps://doi.org/10.2478/sbeef-2023-0014openalex-snapshot
Machine Learning Algorithms Fusion Based on DGA Data for Improving Fault Diagnosis of Electrical Power Transformer
inferred← citeshttps://doi.org/10.36877/pddbs.a0000035openalex-snapshot
An automated workflow by using KNIME Analytical Platform: a case study for modelling and predicting HIV-1 protease inhibitors
inferred← citeshttps://doi.org/10.4155/fsoa-2017-0037openalex-snapshot
Identifying Relationships Between Unrelated Pharmaceutical Target Proteins On the Basis of Shared Active Compounds
inferred← citeshttps://doi.org/10.9734/jpri/2020/v32i4831121openalex-snapshot
VLVS: A Knime Based Virtual Library Generation and Screening Workflow
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