# | Title | Journal | Year | Citations |
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1 | Avogadro: an advanced semantic chemical editor, visualization, and analysis platform | Journal of Cheminformatics | 2012 | 6,063 |
2 | Open Babel: An open chemical toolbox | Journal of Cheminformatics | 2011 | 6,039 |
3 | TCMSP: a database of systems pharmacology for drug discovery from herbal medicines | Journal of Cheminformatics | 2014 | 2,919 |
4 | Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions | Journal of Cheminformatics | 2009 | 786 |
5 | ClassyFire: automated chemical classification with a comprehensive, computable taxonomy | Journal of Cheminformatics | 2016 | 779 |
6 | Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? | Journal of Cheminformatics | 2015 | 775 |
7 | The CompTox Chemistry Dashboard: a community data resource for environmental chemistry | Journal of Cheminformatics | 2017 | 674 |
8 | MetFrag relaunched: incorporating strategies beyond in silico fragmentation | Journal of Cheminformatics | 2016 | 665 |
9 | Molecular de-novo design through deep reinforcement learning | Journal of Cheminformatics | 2017 | 665 |
10 | Mordred: a molecular descriptor calculator | Journal of Cheminformatics | 2018 | 622 |
11 | Cross-validation pitfalls when selecting and assessing regression and classification models | Journal of Cheminformatics | 2014 | 618 |
12 | Organization of GC/MS and LC/MS metabolomics data into chemical libraries | Journal of Cheminformatics | 2010 | 548 |
13 | InChI, the IUPAC International Chemical Identifier | Journal of Cheminformatics | 2015 | 508 |
14 | Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock | Journal of Cheminformatics | 2009 | 445 |
15 | ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database | Journal of Cheminformatics | 2018 | 431 |
16 | CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures | Journal of Cheminformatics | 2011 | 402 |
17 | InChI - the worldwide chemical structure identifier standard | Journal of Cheminformatics | 2013 | 342 |
18 | OPERA models for predicting physicochemical properties and environmental fate endpoints | Journal of Cheminformatics | 2018 | 326 |
19 | Supercell program: a combinatorial structure-generation approach for the local-level modeling of atomic substitutions and partial occupancies in crystals | Journal of Cheminformatics | 2016 | 292 |
20 | The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching | Journal of Cheminformatics | 2017 | 275 |
21 | BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification | Journal of Cheminformatics | 2019 | 269 |
22 | Drug repositioning: a machine-learning approach through data integration | Journal of Cheminformatics | 2013 | 263 |
23 | MOLE 2.0: advanced approach for analysis of biomacromolecular channels | Journal of Cheminformatics | 2013 | 262 |
24 | Open-source platform to benchmark fingerprints for ligand-based virtual screening | Journal of Cheminformatics | 2013 | 243 |
25 | Review on natural products databases: where to find data in 2020 | Journal of Cheminformatics | 2020 | 243 |
26 | ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation | Journal of Cheminformatics | 2015 | 235 |
27 | SimBoost: a read-across approach for predicting drug–target binding affinities using gradient boosting machines | Journal of Cheminformatics | 2017 | 227 |
28 | COCONUT online: Collection of Open Natural Products database | Journal of Cheminformatics | 2021 | 223 |
29 | Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set | Journal of Cheminformatics | 2017 | 219 |
30 | Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models | Journal of Cheminformatics | 2021 | 214 |
31 | P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure | Journal of Cheminformatics | 2018 | 213 |
32 | Confab - Systematic generation of diverse low-energy conformers | Journal of Cheminformatics | 2011 | 211 |
33 | Molecular generative model based on conditional variational autoencoder for de novo molecular design | Journal of Cheminformatics | 2018 | 208 |
34 | JSME: a free molecule editor in JavaScript | Journal of Cheminformatics | 2013 | 204 |
35 | tmChem: a high performance approach for chemical named entity recognition and normalization | Journal of Cheminformatics | 2015 | 203 |
36 | Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data | Journal of Cheminformatics | 2017 | 202 |
37 | Molecular representations in AI-driven drug discovery: a review and practical guide | Journal of Cheminformatics | 2020 | 200 |
38 | A de novo molecular generation method using latent vector based generative adversarial network | Journal of Cheminformatics | 2019 | 198 |
39 | A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions | Journal of Cheminformatics | 2020 | 194 |
40 | Multi-objective de novo drug design with conditional graph generative model | Journal of Cheminformatics | 2018 | 193 |
41 | GNINA 1.0: molecular docking with deep learning | Journal of Cheminformatics | 2021 | 185 |
42 | Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI | Journal of Cheminformatics | 2012 | 179 |
43 | CHEMDNER: The drugs and chemical names extraction challenge | Journal of Cheminformatics | 2015 | 179 |
44 | DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism | Journal of Cheminformatics | 2019 | 174 |
45 | MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics | Journal of Cheminformatics | 2015 | 172 |
46 | The CHEMDNER corpus of chemicals and drugs and its annotation principles | Journal of Cheminformatics | 2015 | 166 |
47 | An open source chemical structure curation pipeline using RDKit | Journal of Cheminformatics | 2020 | 166 |
48 | Building attention and edge message passing neural networks for bioactivity and physical–chemical property prediction | Journal of Cheminformatics | 2020 | 165 |
49 | Randomized SMILES strings improve the quality of molecular generative models | Journal of Cheminformatics | 2019 | 162 |
50 | Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets | Journal of Cheminformatics | 2015 | 160 |