Reconciliation of metabolites and biochemical reactions for metabolic networks"
Thomas Bernard, Alan Bridge, Anne Morgat, Sebastien Moretti, Ioannis Xenarios, and Marco Pagni
Brief Bioinform. 2014; 15(1): p. 123-135 Open Access
- "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
- "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.
- "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
- "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
- "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
- "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)
- "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
- "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)
- "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
- "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)
- "High diversity of soil organic N observed in soil water"
Charles R. Warren
Soil Biol. Biochem. 2012, In Press, available online 18 October 2012
- "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)
- 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
- "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
- "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)
- "Indexing molecules with chemical graph identifiers" (Full Text, PDF)
Elisabet Gregori-Puigjané, Rut Garriga-Sust and Jordi Mestres
J. Comp. Chem. 2011, 32(12), 2638-2646
- "Extending Biochemical Databases by Metabolomic Surveys"
Oliver Fiehn, Dinesh K. Barupal and Tobias Kind
J. Biol. Chem. 2011, 286, 23637-23643
- "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)
- "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)
- "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)
- "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
- "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., accepted for publication, 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
- "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
- "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)
- "The Chemical Translation Service – a web-based tool to improve standardization of metabolomic reports"
Gert Wohlgemuth, Pradeep Kumar Haldiya, Egon Willighagen, Tobias Kind and Oliver Fiehn
Bioinformatics 2010, 26(20), 2647-2648 (Open Access)
- "PathwayAccess: CellDesigner plugins for pathway databases"
John L. Van Hemert and Julie A. Dickerson
Bioinformatics 2010, 26(18), 2345-2346 (Open Access)
- "Utopia documents: linking scholarly literature with research data"
T. K. Attwood, D. B. Kell, P. McDermott, J. Marsh, S. R. Pettifer and D. Thorne
Bioinformatics 2010, 26(18), i568-i574 (Open Access)
- "The INChI as an LSID for molecules in lifescience"
Peter Murray-Rust, Henry Rzepa and Steve Stein
Published online September 2004
- QSAR World article on InChI with references
- "InChI Canonicalization Algorithm"
Depth-First. 2004 published online 12 August 2006