Reference health
Open Babel: An open chemical toolbox
84/84 checkable references clean · checked 2026-07-25
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
24 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 84 checked references that resolve
resolves10.1021/ci00057a005
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
resolves10.1021/ci000404a
Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM
resolves10.1039/b008780g
Development of chemical markup language (CML) as a system for handling complex chemical content
resolves10.1021/ci0502698
Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions
resolves10.1021/ci034207y
Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier
resolves10.1021/ci980335o
Chemical Similarity Assessment through Multilevel Neighborhoods of Atoms: Definition and Comparison with the Other Descriptors
resolves10.1021/c160017a018
The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service.
resolves10.1021/ci000108y
Modular Chemical Descriptor Language (MCDL): Composition, Connectivity, and Supplementary Modules
resolves10.3390/11040219
A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL)
resolves10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
resolves10.1002/(SICI)1096-987X(199604)17:5/6<520::AID-JCC2>3.0.CO;2-W
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
resolves10.1002/(SICI)1096-987X(199604)17:5/6<553::AID-JCC3>3.0.CO;2-T
Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94
resolves10.1002/(SICI)1096-987X(199604)17:5/6<616::AID-JCC5>3.0.CO;2-X
Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules
resolves10.1021/ci100223t
Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress
resolves10.1021/ja00051a040
UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
resolves10.1016/j.jmgm.2005.12.005
Automatic atom type and bond type perception in molecular mechanical calculations
resolves10.1002/prot.21782
A general approach for developing system‐specific functions to score protein–ligand docked complexes using support vector inductive logic programming
resolves10.1007/s10822-008-9241-4
A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank
resolves10.1529/biophysj.107.113860
A Mining Minima Approach to Exploring the Docking Pathways of p-Nitrocatechol Sulfate to YopH
resolves10.1021/ct900262t
An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics
resolves10.1016/j.thromres.2010.08.006
A Series of Natural Flavonoids as Thrombin Inhibitors: Structure-activity relationships
resolves10.1371/journal.pone.0012063
A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways
resolves10.1039/C0MB00148A
Molecular modeling of the human serotonin1Areceptor: role of membranecholesterol in ligand binding of the receptor
resolves10.1021/ci6004178
TMACC: Interpretable Correlation Descriptors for Quantitative Structure−Activity Relationships
resolves10.1186/1471-2105-9-438
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening
resolves10.1021/ci8003418
Bioisosteric Similarity of Molecules Based on Structural Alignment and Observed Chemical Replacements in Drugs
resolves10.1186/1471-2105-11-S3-S8
Application of kernel functions for accurate similarity search in large chemical databases
resolves10.1021/ci100364a
Binary Classification of Aqueous Solubility Using Support Vector Machines with Reduction and Recombination Feature Selection
resolves10.1093/bioinformatics/btp056
Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index
resolves10.1002/prot.22102
Very fast prediction and rationalization of p<i>K</i><sub>a</sub> values for protein–ligand complexes
resolves10.1371/journal.pone.0008057
A Large Scale Analysis of Information-Theoretic Network Complexity Measures Using Chemical Structures
resolves10.1021/jm049113+
Anchor−GRIND: Filling the Gap between Standard 3D QSAR and the GRid-INdependent Descriptors
resolves10.1021/ci0504723
Multifingerprint Based Similarity Searches for Targeted Class Compound Selection
resolves10.1371/journal.pcbi.1000695
Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods
resolves10.1186/1472-6769-9-6
DG-AMMOS: A New tool to generate 3D conformation of small molecules using D istance G eometry and A utomated M olecular M echanics O ptimization for in silico S creening
resolves10.1038/msb4100156
The environmental fate of organic pollutants through the global microbial metabolism
resolves10.1002/jcc.20823
cclib: A library for package‐independent computational chemistry algorithms
resolves10.1186/1752-153X-2-18
DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0
resolves10.1186/1471-2105-9-396
FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects
resolves10.1007/s10994-010-5187-6
Efficient mining for structurally diverse subgraph patterns in large molecular databases
resolves10.1007/s11030-005-9001-5
Lazy structure-activity relationships (lazar) for the prediction of rodent carcinogenicity and Salmonella mutagenicity
resolves10.1002/jcc.20161
OOPSE: An object‐oriented parallel simulation engine for molecular dynamics
resolves10.1007/s00894-010-0684-x
Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields
resolves10.1021/ci800067r
Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution
resolves10.1016/j.cpc.2010.07.048
XtalOpt: An open-source evolutionary algorithm for crystal structure prediction
resolves10.1093/nar/gkr320
ChemMine tools: an online service for analyzing and clustering small molecules
resolves10.1093/nar/gkq969
FragmentStore--a comprehensive database of fragments linking metabolites, toxic molecules and drugs
resolves10.1093/nar/gkq1062
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data
resolves10.1007/s10822-009-9290-3
OpenCDLig: a free web application for sharing resources about cyclodextrin/ligand complexes
resolves10.1093/bioinformatics/btp035
The protein–small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding
resolves10.1002/ejic.200801160
Samb<i>V</i>ca: A Web Application for the Calculation of the Buried Volume of N‐Heterocyclic Carbene Ligands
resolves10.1038/aps.2008.22
ScafBank: a public comprehensive Scaffold database to support molecular hopping
resolves10.1093/bioinformatics/btm363
sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets
resolves10.1093/nar/gkp937
STITCH 2: an interaction network database for small molecules and proteins
resolves10.1007/s10822-005-8694-y
Virtual Computational Chemistry Laboratory – Design and Description
resolves10.1093/nar/gkp324
wwLigCSRre: a 3D ligand-based server for hit identification and optimization
The 24 references without a DOI — listed, not checked
no DOI — not checkedDaylight Theory: : SMARTS http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
no DOI — not checkedFogel K: Producing Open Source Software: How to Run a Successful Free Software Project. 2005, O'Reilly Media, Inc. Sebastopol, CA
no DOI — not checkedCitations were generated by Google Scholar: [http://scholar.google.com/scholar?as_q=openbabel&num=10&as_occt=any&as_publication=&as_ylo=2001]
no DOI — not checkedA selection of such projects is included below. : The full list is available at: http://openbabel.org/wiki/Related_Projects
no DOI — not checkedOpen Babel: : [http://openbabel.org/]
no DOI — not checkedOpen Babel Report Format: : [http://openbabel.org/docs/2.3.0/FileFormats/Open_Babel_report_format.html]
no DOI — not checkedOpen Babel Fingerprint Format: : [http://openbabel.org/docs/2.3.0/FileFormats/Fingerprint_format.html]
no DOI — not checkedOpen Babel Fastsearch Format: : [http://openbabel.org/docs/2.3.0/FileFormats/Fastsearch_format.html]
no DOI — not checkedMolPrint2D Format: : [http://openbabel.org/docs/2.3.0/FileFormats/MolPrint2D_format.html]
no DOI — not checkedMNA Format: : [http://openbabel.org/docs/2.3.0/FileFormats/Multilevel_Neighborhoods_of_Atoms_(MNA).html]
no DOI — not checkedPDB Format v3.2: : [http://www.wwpdb.org/documentation/format32/v3.2.html]
no DOI — not checkedPDB: Cruft to Content: : [http://www.daylight.com/meetings/mug01/Sayle/m4xbondage.html]
no DOI — not checkedNauty: : [http://cs.anu.edu.au/~bdm/nauty/]
no DOI — not checkedMcKay BD: Practical graph isomorphism. Congressus Numerantium. 1981, 30: 45-87.
no DOI — not checkedHalgren T, Nachbar R: Merck molecular force field .4. Conformational energies and geometries for MMFF94. J Comput Chem. 1996, 17: 587-615.
no DOI — not checkedCMake: : [http://www.cmake.org/]
no DOI — not checkedMartin K, Hoffman B: Mastering CMake: A Cross-Platform Build System. 2010, Kitware, Inc., Clifton Park, NY, 5
no DOI — not checkedCDash Dashboard for Open Babel: : [http://my.cdash.org/index.php?project=Open+Babel]
no DOI — not checkedOpen Babel Bug Tracker: : [https://sourceforge.net/tracker/?limit=25&func=&group_id=40728&atid=428740&status=2]
no DOI — not checkedDoxygen: : [http://www.doxygen.org/]
no DOI — not checkedOpen Babel API: : [http://openbabel.org/api]
no DOI — not checkedSchietgat L, Ramon J, Bruynooghe M: An Efficiently Computable Graph-Based Metric for the Classification of Small Molecules. Proceedings of the 11th International Conference on Discovery Science. 2008, Springer-Verlag Berlin, Heidelberg, 197-209.
no DOI — not checkedBuehler M, Dodson J, van Duin A: The Computational Materials Design Facility (CMDF): A powerful framework for multi-paradigm multi-scale simulations. Materials Research Society symposium proceedings. 2006, 894: LL3.8-
no DOI — not checkedGreen William, Allen Joshua, Ashcraft Robert, Beran Gregory, Class Caleb, Gao Connie, Franklin Goldsmith C, Harper Michael, Jalan Amrit, Magoon Gregory, Matheu David, Merchant Shamel, Mo Jeffrey, Petway Sarah, Raman Sumathy, Sharma Sandeep, Song Jing, Van Geem Kevin, Wen John, West Richard, Wong Andrew, Wong Hsi-Wu, Yelvington Paul, Yu Joanna: RMG - Reaction Mechanism Generator v3.3. 2011, [http://rmg.sourceforge.net/]
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