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Open Babel: An open chemical toolbox

Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison
2011 Journal of Cheminformatics  
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

Xavier Barbeau, Antony T. Vincent, Patrick Lagüe
2018 Journal of Open Research Software  
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

Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes
2016 Journal of Molecular Graphics and Modelling  
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

Mariana González-Medina, J. Jesús Naveja, Norberto Sánchez-Cruz, José L. Medina-Franco
2017 RSC Advances  
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

Andrey Toropov, Alla Toropova, Anna Lombardo, Alessandra Roncaglioni, Nicoletta Brita, Giovanni Stella, Emilio Benfenati
2012 Open Chemistry  
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

T. W. H. Backman, Y. Cao, T. Girke
2011 Nucleic Acids Research  
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

Norbert Haider
2010 Molecules  
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

Sam Adams, Pablo de Castro, Pablo Echenique, Jorge Estrada, Marcus D Hanwell, Peter Murray-Rust, Paul Sherwood, Jens Thomas, Joe Townsend
2011 Journal of Cheminformatics  
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

Victor E. Itepu, Ogochukwu J. Umezinwa, Fidelis A. Ilukho, Difa A. Collins, Cosmas Samuel
2019 Asian Journal of Research in Biochemistry  
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

SG Hoornaert, N Lassabe, C Finzinger, M Penalva, A Pechstein, J Chirazi, F Mathis
2020 Aeronautics and Aerospace Open Access Journal  
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]

Martin Mann, Heinz Ekker, Christoph Flamm
2013 Lecture Notes in Computer Science  
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

Priyanka Banerjee, Jevgeni Erehman, Björn-Oliver Gohlke, Thomas Wilhelm, Robert Preissner, Mathias Dunkel
2014 Nucleic Acids Research  
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

Jeremy J Yang
2011 Zenodo  
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

Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey R Hutchison
2012 Journal of Cheminformatics  
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]

Yasemin Yesiltepe, Ryan S. Renslow, Thomas O. Metz
2021 arXiv   pre-print
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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