Category Archives : News & Articles

Yong Fuga Li, Kathleen J.S. Tsai, Colin J.B. Harvey, James Jian Li, Beatrice E. Ary, Erin E. Berlew, Brenna L. Boehman, David M. Findley, Alexandra G. Friant, Christopher A. Gardner, Michael P. Gould, Jae H. Ha, Brenna K. Lilley, Emily L. McKinstry, Saadia Nawal, Robert C. Parry, Kristina W. Rothchild, Samantha D. Silbert, Michael D. Tentilucci, Alana M. Thurston, Rebecca B. Wai, Yongjin Yoon, Raeka S. Aiyar, Marnix H. Medema, Maureen E. Hillenmeyer and Louise K. Charkoudian.
Science Direct. 2016 Published online 22 January 2016.

It’s difficult, but important, to make negative predictions

This entry was posted in Articles on February 12, 2016 by Admin.

Richard V. Williams, Alexander Amberg, Alessandro Brigo, Laurence Coquin, Amanda Giddings, Susanne Glowienke, Nigel Greene, Robert Jolly, Ray Kemper, Catherine O’Leary-Steele, Alexis Parenty, Hans-Peter Spirkl, Susanne A. Stalford, Sandy K. Weiner and Joerg Wichard.
Science Direct. 2016 Published online 16 January 2016.

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

This entry was posted in Articles News & Articles on February 12, 2016 by Admin.

Hong Yang, Chu Qin, Ying Hong Li, Lin Tao, Jin Zhou, Chun Yan Yu, Feng Xu, Zhe Chen, Feng Zhu and Yu Zong Chen.
Nucleic Acids Research. 2015 Published online 17 November 2015.

SureChEMBL: a large-scale, chemically annotated patent document database

This entry was posted in Articles on February 12, 2016 by Admin.

George Papadatos, Mark Davie, Nathan Dedman, Jon Chambers, Anna Gaulton, James Siddle, Richard Koks, Sean A. Irvine, Joe Pettersson, Nicko Goncharoff, Anne Hersey, and John P. Overington.
Nucleic Acids Research. 2015 Published online 17 November 2015.

PubChem Substance and Compound databases

This entry was posted in Articles on February 12, 2016 by Admin.

Sunghwan Kim, Paul A. Thiessen, Evan E. Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han, Jane He, Siqian He, Benjamin A. Shoemaker, Jiyao Wang, Bo Yu, Jian Zhang and Stephen H. Bryant.
Nucleic Acids Research. 2015 Published online 22 September 2015.

Databases of Conformations and NMR Structures of Glycan Determinants

This entry was posted in Articles on February 12, 2016 by Admin.

Anita Sarkar, Sophie Drouillard, Alain Rivet and Serge Perez.
Glycobiology. 2015 Published online 3 August 2015.

MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

This entry was posted in Articles on February 12, 2016 by Admin.

Sébastien Moretti, Olivier Martin, T. Van Du Tran, Alan Bridge, Anne Morgat and Marco Pagni.
Nucleic Acids Research. 2015 Published online 2 November 2015.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

This entry was posted in Articles on February 12, 2016 by Admin.

Ron Caspi, Richard Billington, Luciana Ferrer, Hartmut Foerster, Carol A. Fulcher, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne Paley, Pallavi Subhraveti, Daniel S. Weave and Peter D. Karp.
Nucleic Acids Research. 2015 Published online 2 November 2015.

ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli

This entry was posted in Articles on February 12, 2016 by Admin.

Tanvir Sajed, Ana Marcu, Miguel Ramirez, Allison Pon, An Chi Guo, Craig Knox, Michael Wilson, Jason R. Grant, Yannick Djoumbou and David S. Wishart.
Nucleic Acids Research. 2015 Published online 19 October 2015.

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

This entry was posted in Articles on February 12, 2016 by Admin.

Michael K. Gilson, Tiqing Liu, Michael Baitaluk, George Nicola, Linda Hwang and Jenny Chong.
Nucleic Acids Research. 2015 Published online 19 October 2015.

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

This entry was posted in Articles on February 12, 2016 by Admin.

Kai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu and Sebastian Böcker.

PNAS. 2015 Published online 13 October 2015.

The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands

This entry was posted in Articles on February 12, 2016 by Admin.

Christopher Southan, Joanna L. Sharman, Helen E. Benson, Elena Faccenda, Adam J. Pawson, Stephen P. H. Alexander, O. Peter Buneman, Anthony P. Davenport, John C. McGrath, John A. Peters, Michael Spedding, William A. Catterall, Doriano Fabbro and Jamie A. Davies.
Nucleic Acids Research. 2015 Published online 12 October 2015.

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

This entry was posted in Articles on February 12, 2016 by Admin.

Peter D. Karp, Mario Latendresse, Suzanne M. Paley, Markus Krummenacker, Quang D. Ong, Richard Billington, Anamika Kothari, Daniel Weaver, Thomas Lee, Pallavi Subhraveti, Aaron Spaulding, Carol Fulcher, Ingrid M. Keseler and Ron Caspi.
Briefings in Bioinformatics. 2015 Published online 10 October 2015.

Update – Nov 2015

This entry was posted in Updates on November 24, 2015 by Richard Kidd.

Progress update from our Project Director (Nov 2015)

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME

This entry was posted in Articles on September 23, 2015 by Admin.

George Nicola, Michael R. Berthold, Michael P. Hedrick and Michael K. Gilson.
Oxford University Press. 2015 Published online August 2015.

Data Formats for Elementary Gas-Phase Kinetics: Part 3: Reaction Classification

This entry was posted in Articles on July 29, 2015 by Admin.

D. R. Burgess, Jr., J. A. Manion, and C. J. Hayes
International Journal of Chemical Kinetics. 2015; 47, 361-378. Published online 20 April 2015.

Data Formats for Elementary Gas-Phase Kinetics: Part 2. Unique Representations of Reactions

This entry was posted in Articles on July 29, 2015 by Admin.

D. R. Burgess, Jr., J. A. Manion, and C. J. Hayes
International Journal of Chemical Kinetics. 2015; 47, 334-350. Published online 25 March 2015.

Data Formats for Elementary Gas Phase Kinetics, Part 1: Unique Representations of Species at the Molecular Level

This entry was posted in Articles on July 29, 2015 by Admin.

D. R. Burgess, Jr., J. A. Manion, and C. J. Hayes
International Journal of Chemical Kinetics. 2014; 46, 640-650. Published online 26 August 2014.

Chemical biology databases: from aggregation, curation to representation

This entry was posted in Articles on July 29, 2015 by Admin.

Karine Audouze, Olivier Taboureau
Drug Discovery Today: Technologies. 2015. Published online 7 May 2015.

Update – March 2015

This entry was posted in Updates on May 14, 2015 by Richard Kidd.

Progress update from our Project Director (Mar 2015)

Update – August 2014

This entry was posted in Updates on May 14, 2015 by Richard Kidd.

Catch up with our latest Project Director’s Report (August 2014)

Reconciliation of metabolites and biochemical reactions for metabolic networks

This entry was posted in Articles on June 10, 2014 by Administrator.

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.

Chemical annotation of small and peptide-like molecules at the Protein Data Bank

This entry was posted in Articles on December 12, 2013 by Administrator.

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

This entry was posted in Articles on November 28, 2013 by Administrator.

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

This entry was posted in Articles on November 14, 2013 by Administrator.

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)

This entry was posted in Articles on October 24, 2013 by Administrator.

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

This entry was posted in Updates on September 29, 2013 by Administrator.

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)