Thomas Bernard, Alan Bridge, Anne Morgat, Sebastien Moretti, Ioannis Xenarios, and Marco Pagni
Brief Bioinform. 2014; 15(1): p. 123-135 (Open Access). Read the article here.
Author Archives : Administrator
Chemical annotation of small and peptide-like molecules at the Protein Data Bank
Jasmine Y. Young, Zukang Feng, Dimitris Dimitropoulos, Raul Sala, John Westbrook, Marina Zhuravleva, Chenghua Shao, Martha Quesada, Ezra Peisach, and Helen M. Berman
Database. 2013, published online December 2013. Read the article here.
STITCH 4: integration of protein-chemical interactions with user data
Michael Kuhn, Damian Szklarczyk, Sune Pletscher-Frankild, Thomas H. Blicher, Christian von Mering, Lars J. Jensen, and Peer Bork
Nucleic Acids Res. 2013, published online 28 November 2013. Read the article here.
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands
Adam J. Pawson, Joanna L. Sharman, Helen E. Benson, Elena Faccenda, Stephen P.H. Alexander, Peter O. Buneman, Anthony P. Davenport, John C. McGrath, John A. Peters, Christopher Southan, Michael Spedding, Wenyuan Yu, Anthony J. Harmar
Oxford Journals. 2013, published online on 14 November 2013. Read the article here .
International chemical identifier for reactions (RInChI)
Guenter Grethe, Jonathan M Goodman and Chad HG Allen
J. Cheminf. 2013, 5:45, published online on 24 October 2013. Read here.
Update – September 2013
Our recent set of videos are now available on YouTube (and via the home page) – please use them and let us know what you think!
Read the papers from “The IUPAC International Chemical Identifier (InChI) and its influence on the domain of chemical information“, the special issue of J. Cheminf., 2012
Catch up with our latest Project Directors Report (August 2013)
iPfam: a database of protein family and domain interactions found in the Protein Data Bank
Robert D. Finn, Benjamin L. Miller, Jody Clements, and Alex Bateman
Nucleic Acids Res. 2013, published online 1 December 2013. Read the article here.
Knowledge representation in metabolic pathway databases
Miranda D. Stobbe, Gerbert A. Jansen, Perry D. Moerland and Antoine H.C. van Kampen
Brief. Bioinform. 2012, published online on 30 November 2012. Read the article here.
NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database
Manu Mangal, Parul Sagar, Harinder Singh, Gajendra P. S. Raghava and Subhash M. Agarwal
Nucl. Acids Res. 2012, published online on 29 November 2012 (Open Access). Read the article here.
Challenges and recommendations for obtaining chemical structures of industry-provided repurposing candidates
Christopher Southan, Antony J. Williams and Sean Ekins
Drug Discovery Today 2012, published online on 15 November 2012. Read the article here.
Update – October 2012
InChI Trust Project Director’s Newsletter (October 2012)
High diversity of soil organic N observed in soil water
Charles R. Warren
Soil Biol. Biochem. 2012, In Press, available online 18 October 2012. Read the article here.
MetiTree: a web application to organize and process high-resolution multi-stage mass spectrometry metabolomics data
Miguel Rojas-Chertó, Michael van Vliet, Julio E. Peironcely, Ronnie van Doorn, Maarten Kooyman, Tim te Beek, Marc A. van Driel, Thomas Hankemeier and Theo Reijmers
Bioinformatics 2012, 28(20), 2707-2709 (Open Access). Read the article here.
Towards a Universal SMILES representation – A standard method to generate canonical SMILES based on the InChI
Noel M. O’Boyle
J. Chem. Inf. 2012, available online on 18 September 2012.
Genesys: kinetic model construction using chemo-informatics
Nick M. Vandewiele, Kevin M. Van Geem, Marie-Françoise Reyniers and Guy B. Marin
Chem. Eng. J. 2012, available online on 25 July 2012
Prioritization of chemicals in the aquatic environment based on risk assessment: Analytical, modeling and regulatory perspective
D. Guillén, A. Ginebreda, M. Farré, R.M. Darbra, M. Petrovic, M. Gros and D. Barceló
Sci. Total Environ. 2012, available online on 17 July 2012
MetaboSearch: Tool for Mass-Based Metabolite Identification Using Multiple Databases
Bin Zhou, Jinlian Wang and Habtom W. Ressom
PLoS ONE 2012, published online on 29 June 2012
MaConDa: a publicly accessible mass spectrometry contaminants database
Ralf J. M. Weber, Eva Li, Jonathan Bruty, Shan He and Mark R. Viant
Bioinformatics 2012, 28(21), 2856-2857 (Open Access). Read the article here.
Update – March 2012
An all-day symposium dedicated to the International Chemical Identifier (InChI) will be held at the 243rd ACS National Meeting in San Diego, CA. In sixteen presentations (including several talks by InChI Trust members and supporters) the current status and future of the InChI will be discussed and the use and usefulness of InChIs in databases, publications, software and other resources will be presented. The InChI Symposium Speakers Dinner is sponsored by the InChI Trust.
The InChI Symposium takes place in Room 27A of the San Diego Convention Center on Wednesday, 28th March 2012, and starts at 8:30 am.
Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation
Antony J. Williams, Sean Ekins and Valery Tkachenko
Drug Discovery Today 2012, published online on 8 March 2012
InChI – the worldwide chemical structure identifier standard
Stephen Heller, Alan McNaught, Stephen Stein, Dmitrii Tchekhovskoi and Igor Pletnev
J. Cheminf. 2013, 5:7, published online on 24 January 2013 (Open Access).
Update – October 2011
The InChI Trust and the International Union of Pure and Applied Chemistry (IUPAC) are pleased to announce the release of a new version of the IUPAC International Chemical Identifier (InChI) software. Version 1.04 of the open source software is now available on the InChI Trust Download page. This version now supports the chemical elements up to 112, copernicium (the last one which is currently recognized by IUPAC; support for elements 105-112 is newly added). The inchi-1 executable (both Windows and Linux versions) now allows the processing of multiple input files in a single run (common file name wildcards are recognized).
The InChI Certification Suite is now available from the InChI Trust. This software was developed to check that an installation of the InChI program has been performed correctly. More information on the InChI Certification Suite and the contact information can be found here.
New InChI working groups on “Inorganics” and “Biopolymers & Proteins” are planned for 2012.
ChEMBL: a large-scale bioactivity database for drug discovery
Anna Gaulton, Louisa J. Bellis, A. Patricia Bento, Jon Chambers, Mark Davies, Anne Hersey, Yvonne Light, Shaun McGlinchey, David Michalovich, Bissan Al-Lazikani and John P. Overington
Nucl. Acids Res. 2011, published online on 23 September 2011 (Open Access)
Seaweed metabolite database (SWMD): A database of natural compounds from marine algae
G. D. J. Davis and A. H. R. Vasanthi
Bioinformation 2011, 5(8), 361-364. Read the article here.
Indexing molecules with chemical graph identifiers
Elisabet Gregori-Puigjané, Rut Garriga-Sust and Jordi Mestres
J. Comp. Chem. 2011, 32(12), 2638-2646. Read the article here.
GLAMM: Genome-Linked Application for Metabolic Maps
John T. Bates, Dylan Chivian and Adam P. Arkin
Nucl. Acids Res. 2011, published online on 29 May 2011 (Open Access)
Swimming into peptidomimetic chemical space using pepMMsMIMIC
Matteo Floris, Joel Masciocchi, Marco Fanton and Stefano Moro
Nucl. Acids Res. 2011, published online on 27 May 2011 (Open Access)
ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry
Manor Askenazi and Michal Linial
Nucl. Acids Res. 2011, published online on 27 May 2011 (Open Access)
Extending Biochemical Databases by Metabolomic Surveys
Oliver Fiehn, Dinesh K. Barupal and Tobias Kind
J. Biol. Chem. 2011, 286, 23637-23643. Read the article here.
Simplified molecular input-line entry system and International Chemical Identifier in the QSAR analysis of styrylquinoline derivatives as HIV-1 integrase inhibitors
A. P. Toropova, A. A. Toropov, E. Benfenati and G. Gini
Chem. Biol. Drug. Des., 2011 published online.
Tautomer Identification and Tautomer Structure Generation Based on the InChI Code
Torsten Thalheim, Armin Vollmer, Ralf-Uwe Ebert, Ralph Kühne and Gerrit Schüürmann
J. Chem. Inf. Model. 2010, 50(7), 1223-1232. Read the article here.
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data
Joanna L. Sharman, Chidochangu P. Mpamhanga, Michael Spedding, Pierre Germain, Bart Staels, Catherine Dacquet, Vincent Laudet, Anthony J. Harmar and NC-IUPHAR
Nucl. Acids Res. 2010, published online on 17 November 2010 (Open Access)
A list of organic kryptoracemates
Lászlo Fábián and Carolyn Pratt Brock
Acta Cryst. 2010, B66, 94-103. View the article here.
Challenges in integrating Escherichia coli molecular biology data
Anália Lourenço, Sónia Carneiro, Miguel Rocha, Eugénio C. Ferreira and Isabel Rocha
Brief. Bioinform. 2010, published online on 07 November 2010
EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities
Kun-Yi Hsin, Hugh P. Morgan, Steven R. Shave, Andrew C. Hinton, Paul Taylor and Malcolm D. Walkinshaw
Nucl. Acids Res. 2010, published online on 4 November 2010 (Open Access).
The RCSB Protein Data Bank: redesigned web site and web services
Peter W. Rose, Bojan Beran, Chunxiao Bi, Wolfgang F. Bluhm, Dimitris Dimitropoulos, David S. Goodsell, Andreas Prlić, Martha Quesada, Gregory B. Quinn, John D. Westbrook, Jasmine Young, Benjamin Yukich, Christine Zardecki, Helen M. Berman and Philip E. Bourne
Nucl. Acids Res. 2010, published online on 29 October 2010 (Open Access)
ChemProt: a disease chemical biology database
Olivier Taboureau, Sonny Kim Nielsen, Karine Audouze, Nils Weinhold, Daniel Edsgärd, Francisco S. Roque, Irene Kouskoumvekaki, Alina Bora, Ramona Curpan, Thomas Skøt Jensen, Søren Brunak and Tudor I. Oprea
Nucl. Acids Res. 2010, published online on 8 October 2010 (Open Access)
Update – July 2010
The InChI Trust has initiated a contract with GGA Software Services LLC for its subsidiary SciTouch LLC to develop software programs to test and certify that InChIs and InChIKeys produced by whatever means are correct and valid. This work will expand on and make even more robust the original programs developed by NIST as part of the original InChI project. Trust members and others are contributing both large and diverse databases for testing to assure that current and future versions of the InChI software are of the highest possible quality and meet all needs of the community using the InChI algorithms. We expect the testing software to be available in autumn 2010.
Mol files and InChI Keys in Elsevier online articles on ScienceDirect
This article describes the use of Mol files and InChIKeys in the online resources of Elsevier.
Update – June 2010
The InChI Trust and the International Union of Pure and Applied Chemistry (IUPAC) are pleased to announce the release of a new version of the IUPAC International Chemical Identifier (InChI) software. Version 1.03 of the open source software is now available (Download page).
