2013

Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv
Ziehm, Matthias, and Thornton Janet M.
Aging Cell. (2013), doi: 10.1111/acel.12121
Transcriptional feedback in the Insulin Signalling Pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster
Ivanov, Dobril K., Papatheodorou Irene, Ziehm Matthias, and Thornton Janet M.
Mol. BioSyst.. (2013), p.1756–1764 doi: 10.1039/C3MB25485B
The EBI enzyme portal.
Alcántara, Rafael, Onwubiko Joseph, Cao Hong, de Matos Paula, Cham Jennifer A., Jacobsen Jules, Holliday Gemma L., Fischer Julia D., Rahman Syed Asad, Jassal Bijay, et al.
Nucleic Acids Res. Jan, Volume 41, Number Database issue, (2013), p.D773–D780 doi: 10.1093/nar/gks1112
Abstracting knowledge from the protein data bank.
Furnham, Nicholas, Laskowski Roman A., and Thornton Janet M.
Biopolymers. Mar, Volume 99, Number 3, (2013), p.183–188 doi: 10.1002/bip.22107
Protein Data Resources
Furnham, Nicholas, Garavelli John S., and Thornton Janet M.
Encyclopedia of Biological Chemistry. Volume 3, (2013), p.611-617
Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data
Ziehm, Matthias, Piper Matthew D., and Thornton Janet M.
Aging Cell. (2013), doi: 10.1111/acel.12123
The Ramachandran plot and protein structure validation
Laskowski, Roman A., Furnham Nicholas, and Thornton Janet M.
Biomolecular Forms and Functions, A Celebration of 50 years of the Ramachandran Map. (2013), p.62-75
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Sillitoe, Ian, Cuff Alison L., Dessailly Benoit H., Dawson Natalie L., Furnham Nicholas, Lee David, Lees Jonathan G., Lewis Tony E., Studer Romain A., Rentzsch Robert, et al.
Nucleic Acids Res. Jan, Volume 41, Number Database issue, (2013), p.D490–D498 doi: 10.1093/nar/gks1211

2012

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.
Papatheodorou, Irene, Ziehm Matthias, Wieser Daniela, Alic Nazif, Partridge Linda, and Thornton Janet M.
PLoS One. Volume 7, Number 12, (2012), p.e50881 doi: 10.1371/journal.pone.0050881
MACiE: exploring the diversity of biochemical reactions.
Holliday, Gemma L., Andreini Claudia, Fischer Julia D., Rahman Syed Asad, Almonacid Daniel E., Williams Sophie T., and Pearson William R.
Nucleic Acids Res. Jan, Volume 40, Number Database issue, (2012), p.D783–D789 doi: 10.1093/nar/gkr799
Shouldn't enantiomeric purity be included in the 'minimum information about a bioactive entity'?
Lentini, Giovanni
Nat Rev Drug Discov. Sep, Volume 11, Number 9, (2012), p.730; author reply 730 doi: 10.1038/nrd3503-c1
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
Furnham, Nicholas, Sillitoe Ian, Holliday Gemma L., Cuff Alison L., Laskowski Roman A., Orengo Christine A., and Thornton Janet M.
PLoS Comput Biol. Volume 8, Number 3, (2012), p.e1002403 doi: 10.1371/journal.pcbi.1002403
Machine learning scoring functions based on random forest and support vector regression
Ballester, Pedro J.
Pattern Recognition in Bioinformatics. 7th IAPR International Conference, PRIB 2012, Tokyo, Japan, November 8-10, 2012. Proceedings. Volume 7632 LNBI, (2012), p.14-25 doi: 10.1007/978-3-642-34123-6_2
Bioisosteres in Medicinal Chemistry
Ballester, Pedro J., and Brown Nathan
Methods and Principles in Medicinal Chemistry. Volume 54, (2012), p.155-167
Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification.
Ballester, Pedro J., Mangold Martina, Howard Nigel I., Robinson Richard L. Marchese, Abell Chris, Blumberger Jochen, and Mitchell John B. O.
J R Soc Interface. Dec, Volume 9, Number 77, (2012), p.3196–3207 doi: 10.1098/rsif.2012.0569
ELIXIR: a distributed infrastructure for European biological data.
Crosswell, Lindsey C., and Thornton Janet M.
Trends Biotechnol. May, Volume 30, Number 5, (2012), p.241–242 doi: 10.1016/j.tibtech.2012.02.002
Serotonin: from top to bottom.
Fidalgo, Sara, Ivanov Dobril K., and Wood Shona H.
Biogerontology. Oct, (2012), doi: 10.1007/s10522-012-9406-3
Delivering ICT infrastructure for biomedical research
Nyrönen, Tommi Henrik, Laitinen Jarno, Tourunen Olli, Sternkopf Danny, Laurikainen Risto, ster Per Ö., Lehtovuori Pekka T., Miettinen Timo A., Simonen Tomi, Perheentupa Teemu, et al.
Proceedings of the WICSA/ECSA 2012 Companion Volume. (2012), New York, NY, USA, p.37–44 doi: 10.1145/2361999.2362006
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
Furnham, Nicholas, Sillitoe Ian, Holliday Gemma L., Cuff Alison L., Rahman Syed A., Laskowski Roman A., Orengo Christine A., and Thornton Janet M.
Nucleic Acids Res. Jan, Volume 40, Number Database issue, (2012), p.D776–D782 doi: 10.1093/nar/gkr852
Current challenges in genome annotation through structural biology and bioinformatics.
Furnham, Nicholas, de Beer Tjaart A. P., and Thornton Janet M.
Curr Opin Struct Biol. Oct, Volume 22, Number 5, (2012), p.594–601 doi: 10.1016/j.sbi.2012.07.005

2011

Minimum information about a bioactive entity (MIABE).
Orchard, Sandra, Al-Lazikani Bissan, Bryant Steve, Clark Dominic, Calder Elizabeth, Dix Ian, Engkvist Ola, Forster Mark, Gaulton Anna, Gilson Michael, et al.
Nat Rev Drug Discov. Sep, Volume 10, Number 9, (2011), p.661–669 doi: 10.1038/nrd3503
Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice.
Hilton, Jennifer M., Lewis Morag A., Grati M'hamed, Ingham Neil, Pearson Selina, Laskowski Roman A., Adams David J., and Steel Karen P.
Genome Biol. Volume 12, Number 9, (2011), p.R90 doi: 10.1186/gb-2011-12-9-r90
Comments on "leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets": significance for the validation of scoring functions.
Ballester, Pedro J., and Mitchell John B. O.
J Chem Inf Model. Aug, Volume 51, Number 8, (2011), p.1739–1741 doi: 10.1021/ci200057e
The new science of ageing.
Partridge, Linda, Thornton Janet M., and Bates Gillian
Philos Trans R Soc Lond B Biol Sci. Jan, Volume 366, Number 1561, (2011), p.6–8 doi: 10.1098/rstb.2010.0298
Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling.
Alic, Nazif, T. Andrews Daniel, Giannakou Maria E., Papatheodorou Irene, Slack Cathy, Hoddinott Matthew P., Cochemé Helena M., Schuster Eugene F., Thornton Janet M., and Partridge Linda
Mol Syst Biol. Volume 7, (2011), p.502 doi: 10.1038/msb.2011.36
Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.
Holliday, Gemma L., Fischer Julia D., Mitchell John B. O., and Thornton Janet M.
FEBS J. Oct, Volume 278, Number 20, (2011), p.3835–3845 doi: 10.1111/j.1742-4658.2011.08190.x
Celebrating structural biology.
Thornton, Janet M.
Nat Struct Mol Biol. Dec, Volume 18, Number 12, (2011), p.1304–1316
Structural annotation of Mycobacterium tuberculosis proteome.
Anand, Praveen, Sankaran Sandhya, Mukherjee Sumanta, Yeturu Kalidas, Laskowski Roman A., Bhardwaj Anshu, Bhagavat Raghu, Consortium O. S. D. D., Brahmachari Samir K., and Chandra Nagasuma
PLoS One. Volume 6, Number 10, (2011), p.e27044 doi: 10.1371/journal.pone.0027044
Protein structure databases.
Laskowski, Roman A.
Mol Biotechnol. Jun, Volume 48, Number 2, (2011), p.183–198 doi: 10.1007/s12033-010-9372-4
Computational biology for ageing.
Wieser, Daniela, Papatheodorou Irene, Ziehm Matthias, and Thornton Janet M.
Philos Trans R Soc Lond B Biol Sci. Jan, Volume 366, Number 1561, (2011), p.51–63 doi: 10.1098/rstb.2010.0286
Ultrafast shape recognition: method and applications.
Ballester, Pedro J.
Future Med Chem. Jan, Volume 3, Number 1, (2011), p.65–78 doi: 10.4155/fmc.10.280
Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
Cuff, Alison L., Sillitoe Ian, Lewis Tony, Clegg Andrew B., Rentzsch Robert, Furnham Nicholas, Pellegrini-Calace Marialuisa, Jones David, Thornton Janet M., and Orengo Christine A.
Nucleic Acids Res. Jan, Volume 39, Number Database issue, (2011), p.D420–D426 doi: 10.1093/nar/gkq1001
The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides.
McParland, Victoria, Varsano Giulia, Li Xun, Thornton Janet M., Baby Jancy, Aravind Ajay, Meyer Christoph, Pavic Karolina, Rios Pablo, and Köhn Maja
Biochemistry. Sep, Volume 50, Number 35, (2011), p.7579–7590 doi: 10.1021/bi201095z
LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Laskowski, Roman A., and Swindells Mark B.
J Chem Inf Model. Oct, Volume 51, Number 10, (2011), p.2778–2786 doi: 10.1021/ci200227u
1,000 structures and more from the MCSG.
Lee, David, de Beer Tjaart A. P., Laskowski Roman A., Thornton Janet M., and Orengo Christine A.
BMC Struct Biol. Volume 11, (2011), p.2 doi: 10.1186/1472-6807-11-2

2010

Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk.
Slack, Cathy, Werz Christian, Wieser Daniela, Alic Nazif, Foley Andrea, Stocker Hugo, Withers Dominic J., Thornton Janet M., Hafen Ernst, and Partridge Linda
PLoS Genet. Mar, Volume 6, Number 3, (2010), p.e1000881 doi: 10.1371/journal.pgen.1000881
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking.
Ballester, Pedro J., and Mitchell John B. O.
Bioinformatics. May, Volume 26, Number 9, (2010), p.1169–1175 doi: 10.1093/bioinformatics/btq112
On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.
Kahraman, Abdullah, Morris Richard J., Laskowski Roman A., Favia Angelo D., and Thornton Janet M.
Proteins. Apr, Volume 78, Number 5, (2010), p.1120–1136 doi: 10.1002/prot.22633
The (non)malignancy of cancerous amino acidic substitutions.
Talavera, David, Taylor Martin S., and Thornton Janet M.
Proteins. Feb, Volume 78, Number 3, (2010), p.518–529 doi: 10.1002/prot.22574
Heme proteins–diversity in structural characteristics, function, and folding.
Smith, Lorna J., Kahraman Abdullah, and Thornton Janet M.
Proteins. Aug, Volume 78, Number 10, (2010), p.2349–2368 doi: 10.1002/prot.22747
ArchSchema: a tool for interactive graphing of related Pfam domain architectures.
Tamuri, Asif U., and Laskowski Roman A.
Bioinformatics. May, Volume 26, Number 9, (2010), p.1260–1261 doi: 10.1093/bioinformatics/btq119
Protein structure databases.
Laskowski, Roman A.
Methods Mol Biol. Volume 609, (2010), p.59–82 doi: 10.1007/978-1-60327-241-4_4
Domain-ligand mapping for enzymes.
Bashton, Matthew, and Thornton Janet M.
J Mol Recognit. Volume 23, Number 2, (2010), p.194–208 doi: 10.1002/jmr.992
Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins
Berka, Karel, Laskowski Roman A., Hobza Pavel, and Vondrášek Jiří
Journal of Chemical Theory and Computation. Volume 6, Number 7, (2010), p.2191-2203 doi: 10.1021/ct100007y
Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.
Chan, A. W. Edith, Laskowski Roman A., and Selwood David L.
J Med Chem. Apr, Volume 53, Number 8, (2010), p.3086–3094 doi: 10.1021/jm901696w
The European Bioinformatics Institute's data resources.
Brooksbank, Catherine, Cameron Graham, and Thornton Janet M.
Nucleic Acids Res. Jan, Volume 38, Number Database issue, (2010), p.D17–D25 doi: 10.1093/nar/gkp986
The structures and physicochemical properties of organic cofactors in biocatalysis.
Fischer, Julia D., Holliday Gemma L., Rahman Syed A., and Thornton Janet M.
J Mol Biol. Nov, Volume 403, Number 5, (2010), p.803–824 doi: 10.1016/j.jmb.2010.09.018
Visualization of macromolecular structures.
O'Donoghue, Seán I., Goodsell David S., Frangakis Achilleas S., Jossinet Fabrice, Laskowski Roman A., Nilges Michael, Saibil Helen R., Schafferhans Andrea, Wade Rebecca C., Westhof Eric, et al.
Nat Methods. Mar, Volume 7, Number 3 Suppl, (2010), p.S42–S55 doi: 10.1038/nmeth.1427
DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO.
Schuster, Eugene, McElwee Joshua J., Tullet Jennifer M. A., Doonan Ryan, Matthijssens Filip, Reece-Hoyes John S., Hope Ian A., Vanfleteren Jacques R., Thornton Janet M., and Gems David
Mol Syst Biol. Aug, Volume 6, (2010), p.399 doi: 10.1038/msb.2010.54
Mutations at key pore-lining positions differentiate the water permeability of fish lens aquaporin from other vertebrates.
Calvanese, Luisa, Pellegrini-Calace Marialuisa, and Oliva Romina
FEBS Lett. Dec, Volume 584, Number 23, (2010), p.4797–4801 doi: 10.1016/j.febslet.2010.10.058
The CoFactor database: organic cofactors in enzyme catalysis.
Fischer, Julia D., Holliday Gemma L., and Thornton Janet M.
Bioinformatics. Oct, Volume 26, Number 19, (2010), p.2496–2497 doi: 10.1093/bioinformatics/btq442
Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity.
Oliva, Romina, Calamita Giuseppe, Thornton Janet M., and Pellegrini-Calace Marialuisa
Proc Natl Acad Sci U S A. Mar, Volume 107, Number 9, (2010), p.4135–4140 doi: 10.1073/pnas.0910632107
Molecular evolution and functional characterization of Drosophila insulin-like peptides.
Grönke, Sebastian, Clarke David-Francis, Broughton Susan, T. Andrews Daniel, and Partridge Linda
PLoS Genet. Feb, Volume 6, Number 2, (2010), p.e1000857 doi: 10.1371/journal.pgen.1000857
Prospective virtual screening with Ultrafast Shape Recognition: the identification of novel inhibitors of arylamine N-acetyltransferases.
Ballester, Pedro J., Westwood Isaac, Laurieri Nicola, Sim Edith, and W. Richards Graham
J R Soc Interface. Feb, Volume 7, Number 43, (2010), p.335–342 doi: 10.1098/rsif.2009.0170

2009

Small Molecule Subgraph Detector (SMSD) toolkit.
Rahman, Syed Asad, Bashton Matthew, Holliday Gemma L., Schrader Rainer, and Thornton Janet M.
J Cheminform. Volume 1, Number 1, (2009), p.12 doi: 10.1186/1758-2946-1-12
A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
Soranzo, Nicole, Spector Tim D., Mangino Massimo, Kühnel Brigitte, Rendon Augusto, Teumer Alexander, Willenborg Christina, Wright Benjamin, Chen Li, Li Mingyao, et al.
Nat Genet. Nov, Volume 41, Number 11, (2009), p.1182–1190 doi: 10.1038/ng.467
Mapping human metabolic pathways in the small molecule chemical space.
Macchiarulo, Antonio, Thornton Janet M., and Nobeli Irene
J Chem Inf Model. Oct, Volume 49, Number 10, (2009), p.2272–2289 doi: 10.1021/ci900196u
New open drug activity data at EBI
Steinbeck, Christoph, Al-Lazikani B, Hermjakob Henning, Overington John, and Thornton Janet M.
Chemistry Central Journal. Volume 3, Number Suppl 1, (2009), p.O3 doi: 10.1186/1752-153X-3-S1-O3
Understanding the functional roles of amino acid residues in enzyme catalysis.
Holliday, Gemma L., Mitchell John B. O., and Thornton Janet M.
J Mol Biol. Jul, Volume 390, Number 3, (2009), p.560–577 doi: 10.1016/j.jmb.2009.05.015
Protein function annotation by homology-based inference.
Loewenstein, Yaniv, Raimondo Domenico, Redfern Oliver C., Watson James, Frishman Dmitrij, Linial Michal, Orengo Christine, Thornton Janet M., and Tramontano Anna
Genome Biol. Volume 10, Number 2, (2009), p.207 doi: 10.1186/gb-2009-10-2-207
Annotations for all by all - the BioSapiens network.
Thornton, Janet M.
Genome Biol. Volume 10, Number 2, (2009), p.401
Metal-MACiE: a database of metals involved in biological catalysis.
Andreini, Claudia, Bertini Ivano, Cavallaro Gabriele, Holliday Gemma L., and Thornton Janet M.
Bioinformatics. Aug, Volume 25, Number 16, (2009), p.2088–2089 doi: 10.1093/bioinformatics/btp256
Protein Function Prediction from Structure in Structural Genomics and its Contribution to the Study of Health and Disease
Watson, James D., and Thornton Janet M.
From Molecules to Medicines. (2009), p.201-215 doi: 10.1007/978-90-481-2339-1_13
Structure Quality Assurance
Laskowski, Roman A.
Structural Bioinformatics. (2009), p.341-375
Structural analysis of metal sites in proteins: non-heme iron sites as a case study.
Andreini, Claudia, Bertini Ivano, Cavallaro Gabriele, Najmanovich Rafael J., and Thornton Janet M.
J Mol Biol. May, Volume 388, Number 2, (2009), p.356–380 doi: 10.1016/j.jmb.2009.02.052
Remote homology detection using a kernel method that combines sequence and secondary-structure similarity scores.
Wieser, Daniela, and Niranjan Mahesan
In Silico Biol. Volume 9, Number 3, (2009), p.89–103
PDBsum new things.
Laskowski, Roman A.
Nucleic Acids Res. Jan, Volume 37, Number Database issue, (2009), p.D355–D359 doi: 10.1093/nar/gkn860
Alternative splicing of transcription factors' genes: beyond the increase of proteome diversity.
Talavera, David, Orozco Modesto, and de la Cruz Xavier
Comp Funct Genomics. (2009), p.905894 doi: 10.1155/2009/905894
Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures
Berka, Karel, Laskowski Roman A., Riley Kevin E., Hobza Pavel, and Vondrášek Jiří
Journal of Chemical Theory and Computation. Volume 5, Number 4, (2009), p.982-992 doi: 10.1021/ct800508v
The CATH classification revisited–architectures reviewed and new ways to characterize structural divergence in superfamilies.
Cuff, Alison L., Sillitoe Ian, Lewis Tony, Redfern Oliver C., Garratt Richard, Thornton Janet M., and Orengo Christine A.
Nucleic Acids Res. Jan, Volume 37, Number Database issue, (2009), p.D310–D314 doi: 10.1093/nar/gkn877
Integrated Servers for Structure-Informed Function Prediction
Laskowski, Roman A.
From Protein Structure to Function with Bioinformatics. (2009), p.251-272
The structural basis of allosteric regulation in proteins.
Laskowski, Roman A., Gerick Fabian, and Thornton Janet M.
FEBS Lett. Jun, Volume 583, Number 11, (2009), p.1692–1698 doi: 10.1016/j.febslet.2009.03.019
WSsas: a web service for the annotation of functional residues through structural homologues.
Talavera, David, Laskowski Roman A., and Thornton Janet M.
Bioinformatics. May, Volume 25, Number 9, (2009), p.1192–1194 doi: 10.1093/bioinformatics/btp116
Prepublication data sharing.
Birney, Ewan, Hudson Thomas J., Green Eric D., Gunter Chris, Eddy Sean, Rogers Jane, Harris Jennifer R., S. Ehrlich Dusko, Apweiler Rolf, Austin Christopher P., et al.
Nature. Sep, Volume 461, Number 7261, (2009), p.168–170 doi: 10.1038/461168a
Analysis of the substrate-binding site of human carbonyl reductases CBR1 and CBR3 by site-directed mutagenesis.
El-Hawari, Yasser, Favia Angelo D., Pilka Ewa S., Kisiela Michael, Oppermann Udo, Martin Hans-Jörg, and Maser Edmund
Chem Biol Interact. Mar, Volume 178, Number 1-3, (2009), p.234–241 doi: 10.1016/j.cbi.2008.11.004
Protein evolution - Sequence, structure and systems
Sternberg, Michael, Thornton Janet M., and Laskowski Roman A.
Biochemist. Volume 31, Number 3, (2009), p.52-52
11beta-Hydroxysteroid dehydrogenase type 1 inhibitors with oleanan and ursan scaffolds.
Blum, Andreas, Favia Angelo D., and Maser Edmund
Mol Cell Endocrinol. Mar, Volume 301, Number 1-2, (2009), p.132–136 doi: 10.1016/j.mce.2008.08.028
The fine details of evolution.
Laskowski, Roman A., Thornton Janet M., and Sternberg Michael J. E.
Biochem Soc Trans. Aug, Volume 37, Number Pt 4, (2009), p.723–726 doi: 10.1042/BST0370723
Genome and proteome annotation: organization, interpretation and integration.
Reeves, Gabrielle A., Talavera David, and Thornton Janet M.
J R Soc Interface. Feb, Volume 6, Number 31, (2009), p.129–147 doi: 10.1098/rsif.2008.0341
The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space.
Cuff, Alison, Redfern Oliver C., Greene Lesley, Sillitoe Ian, Lewis Tony, Dibley Mark, Reid Adam, Pearl Frances, Dallman Tim, Todd Annabel, et al.
Structure. Aug, Volume 17, Number 8, (2009), p.1051–1062 doi: 10.1016/j.str.2009.06.015
PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
Pellegrini-Calace, Marialuisa, Maiwald Tim, and Thornton Janet M.
PLoS Comput Biol. Jul, Volume 5, Number 7, (2009), p.e1000440 doi: 10.1371/journal.pcbi.1000440
Ribosomal protein S6 kinase 1 signaling regulates mammalian life span.
Selman, Colin, Tullet Jennifer M. A., Wieser Daniela, Irvine Elaine, Lingard Steven J., Choudhury Agharul I., Claret Marc, Al-Qassab Hind, Carmignac Danielle, Ramadani Faruk, et al.
Science. Oct, Volume 326, Number 5949, (2009), p.140–144 doi: 10.1126/science.1177221
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra, John A., Laskowski Roman A., Thornton Janet M., Singh Mona, and Funkhouser Thomas A.
PLoS Comput Biol. Dec, Volume 5, Number 12, (2009), p.e1000585 doi: 10.1371/journal.pcbi.1000585
PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.
Oliva, Romina, Thornton Janet M., and Pellegrini-Calace Marialuisa
Bioinformatics. Dec, Volume 25, Number 23, (2009), p.3183–3184 doi: 10.1093/bioinformatics/btp545
The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative.
Persson, Bengt, Kallberg Yvonne, Bray James E., Bruford Elspeth, Dellaporta Stephen L., Favia Angelo D., Duarte Roser Gonzalez, Jörnvall Hans, Kavanagh Kathryn L., Kedishvili Natalia, et al.
Chem Biol Interact. Mar, Volume 178, Number 1-3, (2009), p.94–98 doi: 10.1016/j.cbi.2008.10.040
Toll-like receptor stimulation differentially regulates vasoactive intestinal peptide type 2 receptor in macrophages.
Herrera, Juan Luis, Gonzalez-Rey Elena, Fernandez-Montesinos Rafael, Quintana Francisco J., Najmanovich Rafael, and Pozo David
J Cell Mol Med. Sep, Volume 13, Number 9B, (2009), p.3209–3217 doi: 10.1111/j.1582-4934.2009.00662.x
Missing in action: enzyme functional annotations in biological databases.
Furnham, Nicholas, Garavelli John S., Apweiler Rolf, and Thornton Janet M.
Nat Chem Biol. Aug, Volume 5, Number 8, (2009), p.521–525 doi: 10.1038/nchembio0809-521