A simple shape characteristic of protein protein recognition

Bioinformatics (2007) 23(7), 789–792 The authors wish to apologize for the omission     

'ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data'

Smilde et al. Bioinformatics (2005), 21(13); 3043–3048 The above paper by Smilde et al. inappropriately quotes results     

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks

Bioinformatics (2006) 22(23), 2968–2970 The authors would like     

BIB's first impact factor is 24.37

We are delighted to announce that Briefings in Bioinformaticshas just received its first impact factor—of 24.37! This is a fantastic achievement for the journal, and surelya reflection of     

A new publisher for Briefings in Bioinformatics

This is the first issue of Briefings in Bioinformatics to bepublished by the journal's new publisher, Oxford Journals, adivision of Oxford University Press. Briefings in Bioinformatics,and its sister journal      

Editorial

The first 150 words of the full text of this article appear below. THE RICH DIVERSITY OF GENOMICS—A REPORT ON THE ‘COMPARATIVE AND FUNCTIONAL GENOMICS (BITS) WORKSHOP’, HINXTON, UK, 27–30 OCTOBER 2005 The Comparative and Functional Genomics (BITS) Workshop hasa history that in many ways reflects the changing face of moderngenomics. Started 15 years ago under the banner of ‘Identificationof the Transcribed Sequence’, the meeting was designedto bring together leading researchers from around the worldwho were pioneering new global approaches to gene discoveryin a small workshop setting. As more and more transcribed sequencesbecame known, the emphasis of the meeting, like the communityit served, focused on how to characterize the function of allthe newly acquired genes. A decision was therefore made to changeits name to ‘Beyond the Identification of the TranscribedSequence Workshop’, or BITS for short. As the years havepassed the meeting has continued to diversify and change (ashas its name), but it has continued to attract scientists tothe cutting edge of genomics research. At this year's meeting,hosted . . . [Full Text of this Article]     

Maximum likelihood of phylogenetic networks

Bioinformatics (2006) 22(21), 2604–2611 The authors would like to apologize for errors of graph misplacementin Figures 4–6, and an     

Rhythmic and Light-Inducible Appearance of Clock-Associated Pseudo-Response Regulator Protein PRR9 through Programmed Degradation in the Dark in Arabidopsis thaliana

The above article was published in Plant and Cell Physiology48(11): 1644–1651. Figure 1 was shown incorrectly online. The figure legend inFigure 1C was missing. The correct figure is given below. View larger version (26K):   Fig. 1 Construction     

Observation of multiple folding pathways of beta-hairpin trpzip2 from independent continuous folding trajectories

Motivation: After 10-year investigations, the folding mechanismsof β-hairpins are still under debate. Experiments stronglysupport zip-out pathway, while most simulations prefer the hydrophobiccollapse model (including middle-out and zip-in pathways). Inthis article, we show that all pathways can occur during thefolding of β-hairpins but with different probabilities.The zip-out pathway is the most probable one. This is in agreementwith the experimental results. We came to our conclusions by38 100-ns room-temperature all-atom molecular dynamics simulationsof the β-hairpin trpzip2. Our results may help to clarifythe inconsistencies in the current pictures of β-hairpinfolding mechanisms. Contact: yxiao{at}mail.hust.edu.cn Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Anna Tramontano     

EDITORIAL

The Annals of Botany, one of the oldest botanical journals incontinuous publication, publishes eclectic and innovative papers,both on-line and in print, in almost every sphere of plant biology.Its policy has been and remains to improve and develop all aspectsof the Journal’s provision for the benefit of authorsand readers alike. In doing so, it aims to meet fully theirdemands for a high level of originality in scientific content,top quality reproduction and prompt publication with wide accessibility.Annals of Botany faces these     

Current progress in bioinformatics 2007

Briefings in Bioinformatics is pleased to present our thirdannual ‘Current Progress in Bioinformatics’ specialissue. As in previous years, we have attempted to identify excitingor emerging fields of bioinformatics, and have asked leadersin these fields to present a brief summary of progress overthe last 18–24 months and an annotated biography drawingattention to papers of particular significance. Each year, we have a logistical task of setting the order ofthe articles to appear in this volume. Typically, we organizethem based on the linear logic of biology's central dogma: fromDNA to RNA to protein to function and phenotype. The centraldogma has undergone a transformation in the     

Society for Molecular Biology and Evolution (SMBE) Council and Business Meetings, 2004 State College, Pennsylvania, USA

Council Meeting

1. Call to order.—President John Avise called the meetingto order at 9:00 AM, 17 June 2004. In attendance were PresidentJohn Avise, Treasurer Marta L. Wayne, Editorial Advisory Boardmember Stanley A. Sawyer, Editor William Martin, Past- PresidentNaoyuki Takahata, Secretary Sudhir Kumar, and Councillors G.Brian Golding, Laura A. Katz, and Jody Hey. President-ElectJeffrey R. Powell arrived later due to flight delays. The meetingbegan with Introductions.
2. Approval of minutes.—Councilapproved the minutes of the2003 Council and Business meetings,published in the December2003 issue of the journal MolecularBiology and Evolution (MBE).
3. Editor's report.—Most ofthe meeting addressed a discussionconcerning the Journal'sfuture and dealings with the OxfordUniversity Press (OUP) (seereport).
4. Treasurer's report.—Treasurer Marta L. Waynesummarizedthe financial state of the Society (see report).The fiscalyear has now changed to January–December (coincidentwith     

Society for Molecular Biology and Evolution Council and Business Meetings, 2002

Council Meeting, 2002 Call to order.—The SMBE Council met during two sessionsat the Sorrento Hilton, Sorrento, Italy. President Michael Cleggcalled the first session to order at 1:37 p.m. on June 13, 2002and the second at 1:15 p.m. on June 14, 2002. In attendanceat the first session were Councilor Montserrat Aguadé,President Michael Clegg, Editor Simon Easteal, Treasurer DickHudson, and Secretary Marcy Uyenoyama; these Council memberswere joined at the second session by President-Elect NaoyukiTakahata. S. Blair Hedges, organizer of the 2004 annual meetings,made a     

Can sugars be produced from fatty acids? A test case for pathway analysis tools

Motivation: In recent years, several methods have been proposedfor determining metabolic pathways in an automated way basedon network topology. The aim of this work is to analyse thesemethods by tackling a concrete example relevant in biochemistry.It concerns the question whether even-chain fatty acids, beingthe most important constituents of lipids, can be convertedinto sugars at steady state. It was proved five decades agothat this conversion using the Krebs cycle is impossible unlessthe enzymes of the glyoxylate shunt (or alternative bypasses)are present in the system. Using this example, we can comparethe various methods in pathway analysis. Results: Elementary modes analysis (EMA) of a set of enzymescorresponding to the Krebs cycle, glycolysis and gluconeogenesissupports the scientific evidence showing that there is no pathwaycapable of converting acetyl-CoA to glucose at steady state.This conversion is possible after the addition of isocitratelyase and malate synthase (forming the glyoxylate shunt) tothe system. Dealing with the same example, we compare EMA withtwo tools based on graph theory available online, PathFindingand Pathway Hunter Tool. These automated network generatingtools do not succeed in predicting the conversions known fromexperiment. They sometimes generate unbalanced paths and revealproblems identifying side metabolites that are not responsiblefor the carbon net flux. This shows that, for metabolic pathwayanalysis, it is important to consider the topology (includingbimolecular reactions) and stoichiometry of metabolic systems,as is done in EMA. Contact: ldpf{at}minet.uni-jena.de; schuster{at}minet.uni-jena.de Supplementary information: Supplementary data are availableat Bioinformatics online. FOOTNOTES Associate Editor: Alfonso Valencia Received on July 24, 2008; revised on September 18, 2008; accepted on September 18, 2008     

3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm

Motivation: Reliable structural modelling of protein–proteincomplexes has widespread application, from drug design to advancingour knowledge of protein interactions and function. This workaddresses three important issues in protein–protein docking:implementing backbone flexibility, incorporating prior indicationsfrom experiment and bioinformatics, and providing public accessvia a server. 3D-Garden (Global And Restrained Docking ExplorationNexus), our benchmarked and server-ready flexible docking system,allows sophisticated programming of surface patches by the uservia a facet representation of the interactors’ molecularsurfaces (generated with the marching cubes algorithm). Flexibilityis implemented as a weighted exhaustive conformer search foreach clashing pair of molecular branches in a set of 5000 modelsfiltered from around 340 000 initially. Results: In a non-global assessment, carried out strictly accordingto the protocols for number of models considered and model qualityof the Critical Assessment of Protein Interactions (CAPRI) experiment,over the widely-used Benchmark 2.0 of 84 complexes, 3D-Gardenidentifies a set of ten models containing an acceptable or bettermodel in 29/45 test cases, including one with large conformationalchange. In 19/45 cases an acceptable or better model is rankedfirst or second out of 340 000 candidates. Availability: http://www.sbg.bio.ic.ac.uk/3dgarden (server) Contact: v.lesk{at}ic.ac.uk Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Burkhard Rost     

Editorial note

It has come to the attention of the Executive Editors of Bioinformaticsthat there is significant overlap between the following publications: Rodin A, Mosley TH Jr, Clark AG, Sing