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Open Babel: An open chemical toolbox
2011
Journal of Cheminformatics
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Results: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. ...
Conclusions: Open Babel presents a solution to the proliferation of multiple chemical file formats. ...
Acknowledgements and Funding We would like to thank all users and contributors to the Open Babel project over its history, including OpenEye Scientific Software Inc. for their initial OELib code. ...
doi:10.1186/1758-2946-3-33
pmid:21982300
pmcid:PMC3198950
fatcat:mlbktndtlbactm4wszaft7yqpm
ConfBuster: Open-Source Tools for Macrocycle Conformational Search and Analysis
2018
Journal of Open Research Software
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In addition to Python and the optional R programming languages with freely available packages, the tools require Open Babel and PyMOL to work properly. ...
Macrocycles are cyclic macromolecules that have gained an increased interest in drug development. ...
Acknowledgements A.T.V. received an Alexander Graham Bell Canada Graduate Scholarships from the NSERC. ...
doi:10.5334/jors.189
fatcat:a2s4cn5nhbht3cnokujoxzphly
Open source molecular modeling
2016
Journal of Molecular Graphics and Modelling
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An updated online version of this catalog can be found at https:// opensourcemolecularmodeling.github.io. ...
In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. ...
Galaxy [41] is a web platform for exploring biomedical data and includes as a component a Chemical Toolbox that integrates a number of other cheminformatics tools to offer an array of molecular search ...
doi:10.1016/j.jmgm.2016.07.008
pmid:27631126
pmcid:PMC5037051
fatcat:jxdvghsiszadjevub22qbjywwm
Open chemoinformatic resources to explore the structure, properties and chemical space of molecules
2017
RSC Advances
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Open chemoinformatic servers facilitate analysis of chemical space and structure–activity relationships. ...
and molecular properties
calculation
The server integrates over 30
chemoinformatics and data mining
tools, being ChemMineR, an R package
that integrates Open Babel and JOELib
functionalities, ...
Compound ngerprints are
generated with Open Babel
23
FAF-Drugs4
Mining and ltering chemical
compound libraries
Filters compounds based on
physicochemical properties,
ADMET rules and pan assay ...
doi:10.1039/c7ra11831g
fatcat:jxncc4n6zzgltjzeus5cswh4sy
CORAL: the prediction of biodegradation of organic compounds with optimal SMILES-based descriptors
2012
Open Chemistry
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These six models were further tested against a set of chemicals (n=285) for which only categorical values (biodegradable or not) were available. ...
Thus, this exercise can be considered as both an example of the use of the model as a classifier and as an external validation study. ...
Table 1 contains an example of the calculation of the optimal descriptor (Split 1). ...
doi:10.2478/s11532-012-0031-4
fatcat:kr7uqht6hna37ovypzvgoxlfla
ChemMine tools: an online service for analyzing and clustering small molecules
2011
Nucleic Acids Research
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ChemMine Tools is an online service for small molecule data analysis. ...
Fourth, the service includes a Clustering Toolbox that integrates cheminformatic algorithms with data mining utilities to enable systematic structure and activity based analyses of custom compound sets ...
ACKNOWLEDGEMENTS We thank the community projects-Open Babel, JOELib, CACTVS and R-for providing excellent software and data resources that are used by ChemMine Tools. ...
doi:10.1093/nar/gkr320
pmid:21576229
pmcid:PMC3125754
fatcat:3va53vufe5efxcx3wx3w63ak6a
Functionality Pattern Matching as an Efficient Complementary Structure/Reaction Search Tool: an Open-Source Approach
2010
Molecules
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An open-source software package for creating and operating web-based structure and/or reaction databases is presented. ...
search functionality and other features of -chemical intelligence‖ by extending the syntax of the Structured Query Language (SQL), e.g., via integration of the Open Babel chemistry toolbox [10] . ...
This article is an Open Access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/). ...
doi:10.3390/molecules15085079
pmid:20714286
pmcid:PMC6257694
fatcat:opwvnm6ow5byfk3x3nbajupvh4
The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age
2011
Journal of Cheminformatics
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The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an ...
Such an infrastructure offers benefits at many levels. ...
Avogadro Avogadro is an open source, cross-platform desktop application to manipulate and visualize chemical data in 3D. ...
doi:10.1186/1758-2946-3-38
pmid:21999363
pmcid:PMC3206452
fatcat:v62urvg22rdurbgum6eg4ballq
The Effect of Structural Modification on the Blood Brain Barrier Permeation Properties of Allicin
2019
Asian Journal of Research in Biochemistry
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Nutriceutical allicin is an organice compound gotten from garlic. It is also sourced from onions, and different species in the family Alliaceae. ...
Open Babel, a chemical toolbox is designed to speak many of the languages of chemical data [18] . ...
An open chemical toolbox. Journal of Cheminformatics. 2011;3:33. 19. Bultinck P, Langenaeker W, Lahorte P, De Proft F, Geerlings P, Van Alsenoy C, Tollenaere JP. ...
doi:10.9734/ajrb/2019/v5i330092
fatcat:3idzuwxrm5fhtk4vya2lnilbca
Nature can inspire solutions for aeronautics and space sciences
2020
Aeronautics and Aerospace Open Access Journal
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Aeronautics and Aerospace Open Access Journal Perspective Open Access Nature can inspire solutions for aeronautics and space sciences 70 ...
This promises to open a new era of highly efficient innovation in aeronautics and space science. ...
(Using BABELE? 1 )
2. ...
doi:10.15406/aaoaj.2020.04.00109
fatcat:a6w7zoetmfbhfhlxj5ocixsn7y
The Graph Grammar Library - A Generic Framework for Chemical Graph Rewrite Systems
[chapter]
2013
Lecture Notes in Computer Science
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Furthermore the entire functionality of the popular chemical toolbox Open Babel [5] can be harnessed from within the GGL via the implementation of a bi-directional interface for the exchange of chemical ...
Such a graph grammar is a generating system for the explicit construction of an entire chemical space, Fig. 1 . ...
doi:10.1007/978-3-642-38883-5_5
fatcat:a6njuspuijdknjnsrc7wtyjkom
Super Natural II—a database of natural products
2014
Nucleic Acids Research
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For most of its functions, MyChem relies on the Open Babel toolbox (http: //openbabel.org). ...
For the substructure search, a fast-search index for all database compounds was created using Open Babel (28) . ...
doi:10.1093/nar/gku886
pmid:25300487
pmcid:PMC4384003
fatcat:y25eyjcn6zfplisglawwhy3tni
Cheminformatics Software Development: Case Studies
2011
Zenodo
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From guest lecture presented to IU SOIC I571 "Chemical Information Technology" class, invited by Prof David Wild. ...
H0;#7,#8,#9]' -n_inmax <N> ... input limit -n_outmax <N> -v indicators of community ... output limit ... verbose health -vv ... very verbose *"Open Babel: An open chemical toolbox", Noel M. ...
Daylight Chemical Information Systems, Inc. l Scientific mission: To effectively store, retrieve, process all existing chemical information. l This mission often guided what to do, and also what to not ...
doi:10.5281/zenodo.5585346
fatcat:sb5gaslaarbjlgcte35dbjvwvi
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
2012
Journal of Cheminformatics
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Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net. ...
For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, ...
With over 270,000 downloads, language translations and localizations, and over 100 citations, it has become an integral part of the chemical software toolbox. ...
doi:10.1186/1758-2946-4-17
pmid:22889332
pmcid:PMC3542060
fatcat:e2mdy6dfjfai5gcnexaaiyvjg4
SPECTRe: Substructure Processing, Enumeration, and Comparison Tool Resource: An efficient tool to encode all substructures of molecules represented in SMILES
[article]
2021
arXiv
pre-print
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and chemical classes. ...
Functional groups and moieties are chemical descriptors of biomolecules that can be used to interpret their properties and functions, leading to the understanding of chemical or biological mechanisms. ...
FP2 is a path-based fingerprint, available in Open Babel, an open-source chemical informatics toolbox [54] . FP2 consists of 1024 bits and indexes linear segments of the maximum length of 7 atoms. ...
arXiv:2111.03227v1
fatcat:hiw7csyflnci3hhcyq5fspoi3a
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