The DOI matches its Crossref record.
Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited
Abstract
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDescription of several chemical structure file formats used by computer programs developed at Molecular Design LimitedArthur Dalby, James G. Nourse, W. Douglas Hounshell, Ann K. I. Gushurst, David L. Grier, Burton A. Leland, and John LauferCite this: J. Chem. Inf. Comput. Sci. 1992, 32, 3, 244–255Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://doi.org/10.1021/ci00007a012Request reuse permissionsArticle Views2878Altmetric-Citations470LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) Get e-Alerts
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
PubChem Substance and Compound databases
Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv951 · Cited by 5,436
A Medicinal Chemist’s Guide to Molecular Interactions
Bissantz, C., Kuhn, B., & Stahl, M. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm100112j · Cited by 1,731
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy
Djoumbou Feunang, Y., Eisner, R., Knox, C., Chepelev, L., Hastings, J., Owen, G., Fahy, E., Steinbeck, C., Subramanian, S., Bolton, E., et al. (2016) · Journal of Cheminformatics · doi:10.1186/s13321-016-0174-y · Cited by 1,525
REFMAC 5 dictionary: organization of prior chemical knowledge and guidelines for its use
Vagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F., & Murshudov, G. N. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904023510 · Cited by 1,350
Filimonov, D. A., Lagunin, A. A., Gloriozova, T. A., Rudik, A. V., Druzhilovskii, D. S., Pogodin, P. V., & Poroikov, V. V. (2014) · Chemistry of Heterocyclic Compounds · doi:10.1007/s10593-014-1496-1 · Cited by 1,346
The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics
Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., & Willighagen, E. (2003) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci025584y · Cited by 1,108
InChI, the IUPAC International Chemical Identifier
Heller, S. R., McNaught, A., Pletnev, I., Stein, S., & Tchekhovskoi, D. (2015) · Journal of Cheminformatics · doi:10.1186/s13321-015-0068-4 · Cited by 867
ChEMBL web services: streamlining access to drug discovery data and utilities
Davies, M., Nowotka, M., Papadatos, G., Dedman, N., Gaulton, A., Atkinson, F., Bellis, L., & Overington, J. P. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv352 · Cited by 757
Hsin, K.-Y., Ghosh, S., & Kitano, H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0083922 · Cited by 606
Molecular representations in AI-driven drug discovery: a review and practical guide
David, L., Thakkar, A., Mercado, R., & Engkvist, O. (2020) · Journal of Cheminformatics · doi:10.1186/s13321-020-00460-5 · Cited by 587
Willighagen, E. L., Mayfield, J. W., Alvarsson, J., Berg, A., Carlsson, L., Jeliazkova, N., Kuhn, S., Pluskal, T., Rojas-Chertó, M., Spjuth, O., et al. (2017) · Journal of Cheminformatics · doi:10.1186/s13321-017-0220-4 · Cited by 527
Polymer Genome: A Data-Powered Polymer Informatics Platform for Property Predictions
Kim, C., Chandrasekaran, A., Huan, T. D., Das, D., & Ramprasad, R. (2018) · The Journal of Physical Chemistry C · doi:10.1021/acs.jpcc.8b02913 · Cited by 513
InChI - the worldwide chemical structure identifier standard
Heller, S., McNaught, A., Stein, S., Tchekhovskoi, D., & Pletnev, I. (2013) · Journal of Cheminformatics · doi:10.1186/1758-2946-5-7 · Cited by 477
AceDRG: a stereochemical description generator for ligands
Long, F., Nicholls, R. A., Emsley, P., Gražulis, S., Merkys, A., Vaitkus, A., & Murshudov, G. N. (2017) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798317000067 · Cited by 398
Recent advances in computer-aided drug design
Song, C. M., Lim, S. J., & Tong, J. C. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp023 · Cited by 344
Heteroaromatic Rings of the Future
Pitt, W. R., Parry, D. M., Perry, B. G., & Groom, C. R. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm801513z · Cited by 332
DrugCentral: online drug compendium
Ursu, O., Holmes, J., Knockel, J., Bologa, C. G., Yang, J. J., Mathias, S. L., Nelson, S. J., & Oprea, T. I. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw993 · Cited by 323
Information retrieval and text mining technologies for chemistry
Krallinger, M., Rabal, O., Lourenço, A., Oyarzabal, J., & Valencia, A. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00851 · Cited by 281
Varnek, A., Fourches, D., Hoonakker, F., & Solov’ev, V. P. (2005) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-005-9008-0 · Cited by 208
Deep learning allows genome-scale prediction of Michaelis constants from structural features
Kroll, A., Engqvist, M. K. M., Heckmann, D., & Lercher, M. J. (2021) · PLOS Biology · doi:10.1371/journal.pbio.3001402 · Cited by 132
Updates in Rhea—An expert curated resource of biochemical reactions
Morgat, A., Lombardot, T., Axelsen, K. B., Aimo, L., Niknejad, A., Hyka-Nouspikel, N., Coudert, E., Pozzato, M., Pagni, M., Moretti, S., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw990 · Cited by 65
New prediction categories in CASP15
Kryshtafovych, A., Antczak, M., Szachniuk, M., Zok, T., Kretsch, R. C., Rangan, R., Pham, P., Das, R., Robin, X., Studer, G., et al. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26515 · Cited by 54
“38 Subsequently, the Mol objects are written to the MDL-formatted file, 33 which can be used as a ligand submission template.”
MethodClark, A. M., Williams, A. J., & Ekins, S. (2015) · Journal of Cheminformatics · doi:10.1186/s13321-015-0057-7 · Cited by 33
“For example, MDL Molfiles provide a number of capabilities for specifying chemical queries [55] as atom and bond annotations.”
BackgroundAssessment of tautomer distribution using the condensed reaction graph approach
Gimadiev, T. R., Madzhidov, T. I., Nugmanov, R. I., Baskin, I. I., Antipin, I. S., & Varnek, A. (2018) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-018-0101-6 · Cited by 25
A fully automated benchmarking suite to compare macromolecular complexes
Studer, G., Robin, X., Bienert, S., Durairaj, J., Škrinjar, P., Tauriello, G., Waterhouse, A. M., & Schwede, T. (2026) · Nature Methods · doi:10.1038/s41592-025-02973-z · Cited by 10
“However, the recommended approach is to load ligand structures from SDF files 61 , which inherently provide detailed connectivity information.”
New prediction categories in CASP15
Kryshtafovych, A., Antczak, M., Szachniuk, M., Zok, T., Kretsch, R. C., Rangan, R., Pham, P., Das, R., Robin, X., Studer, G., et al. (2023) · doi:10.22541/au.168371643.39402261/v1 · Cited by 4
Metadata
- Authors
- Dalby, A., Nourse, J. G., Hounshell, W. D., Gushurst, A. K. I., Grier, D. L., Leland, B. A., & Laufer, J.
- Venue
- Journal of Chemical Information and Computer Sciences
- Publisher
- American Chemical Society (ACS)
- Published
- 1992-05-01
- Volume
- 32
- Issue
- 3
- Pages
- 244-255
- ISSN
- 0095-2338 (ISSN-L)
- 1520-5142
- OpenAlex
- W2051810242
- Cited by
- 642
- References
- 0
- FWCI
- 4.19
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
