Robert B Russell

..Recent advances and applications of these methods emphasize the need for hybrid approaches that combine a variety of data to achieve better efficiency, accuracy, resolution and completeness...

..The database also contains Gene Ontology-based functional annotations and interactions between yeast proteins from large-scale interaction discovery studies. A web-based tool to query 3did is available at http://3did.embl.de...

..These regions also offer new possibilities into how interactions can be targeted by small molecules...

..We estimate that there are dozens or even hundreds of linear motifs yet to be discovered that will give molecular insight into protein networks and greatly illuminate cellular processes...

..We also provide worked examples showing how these tools can have an impact on the understanding of protein function prior to experimental studies...

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..We also consider interactions between complexes (cross-talk) and use these to construct a structure-based network of molecular machines in the cell...

..While the screen is likely to miss some targets, our study shows that valid targets can be identified from sequence alone...

..The method, and associated statistics, is an excellent tool for predicting and studying binding sites for newly discovered peptides mediating critical events in biology...

..GlobPlot has a pipeline interface--GlobPipe--for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity...

..To produce the best models, new prediction methods have to somehow combine partial structures with a mixed bag of experimental data, including interactions and low-resolution electron microscopy images...

..For contact predictions, accuracies are still low, although there were several instances of accurate and useful contacts predicted de novo, and new approaches hint at future progress...

..The data set provides a blueprint of the minimal cellular machinery required for life...

..The tool is freely available via a web interface (http://dis.embl.de) and can be downloaded for use in large-scale studies...

..We also discuss the rare instances of fold similarities interacting the same way, and those where obviously homologous proteins interact differently...

..This mutually exclusive expression argues that microRNAs confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions...

..The results are displayed via a visual interface for easy perusal. The server is available at http://dilimot.embl.de...

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..This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling...

..Concurrently, other work has demonstrated that it is possible to target these interactions using small molecules. Together these developments hold great promise for future efforts to target chemically precise details of complex systems...

..InterPreTS includes a useful interface for visualising molecular details of any predicted interaction. AVAILABILITY: http://www.russell.embl.de/interprets...

..This model gives insights into the dynamic properties of full-length ERalpha and into the structure of unliganded ERalpha...

..We currently know fewer than 2,000, and at the present rate of structure determination, it will be more than 20 years before we know a full representative set...

..The approach is applied weekly to all new structures, providing a resource for those interested in using structure to infer function...

..The growth rate of confident predictions is twice that of experimental complexes, meaning that a complete structural drug-protein repertoire will be available at least ten years earlier than by X-ray and NMR techniques alone...

..The results underscore the importance of protein modularity in complex organization, as well as the role of irregular or disordered parts of proteins in crucial biological processes...

..The results imply previously unreported hidden layers of post-transcriptional regulation intertwining phosphorylation with lysine acetylation and other mechanisms that define the functional state of a cell...

..g. in the hydrophobic core). Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities...

..We suggest a process of zooming on the cell, from global networks through pathways to the precise atomic contacts at the interfaces of interacting proteins...

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..The approach is highly complementary to fold comparison for providing functional clues for new structures, and is key for the detection of recurrences of any new pattern...

..To aid functional annotation of proteins, we allow comparisons of pre-defined patterns against databases of complete structures and of entire structures to databases of particular residues likely to be functionally important...

..Structural comparisons, furthermore, establish an evolutionary link to the triosephosphate isomerases, a superfamily hitherto considered independent from the superfamily of aldolases...

..We quantify the associated increase in structural information in Swissprot and discuss examples illustrating the applicability of this approach to understand functional and evolutionary relationships between protein families...

..A report on the Genomics, Proteomics and Bioinformatics for Medicine (GPBM) 2002 meeting, St. Petersburg to Moscow, Russia, 22-30 June 2002...

..We provide confirmation for several interactions, in addition to suggesting molecular details of how they occur...

..In this minireview, we discuss these data, and the issues of turning them into whole cell models...

..We discuss the WD40 domain distributions in protein networks and structures of WD40-containing assemblies to demonstrate their versatility in mediating critical cellular functions...

..We used the structure-based sequence alignment containing residues specific to HPrK/PCK to identify additional members of this P-loop containing family...

..The model suggests numerous experiments to probe exosome function, particularly with respect to subunits making direct atomic contacts and conserved, possibly functional residues within the predicted central pore of the complex...

..For some countries, changes over a four year period appear to correlate with world events related to conflicts or economic problems...

..We propose that projects to uncover the protein-peptide repertoire used in Nature in a systematic way will have numerous applications in molecular biology and medicine...

..The differences of ACMV and MSV virion shapes are discussed with reference to their different animal vectors...

..In this Minireview, we discuss various aspects of these critically important functional regions...

..As a result, we have a more complete view of how many complexes are in living systems, what they look like and the roles they play in the cell...

..Thus, we propose that our structure represents a product/substrate mimic of the kinase/phosphatase reaction...

..A reduction in infectivity caused by mutating one member of a significant pair could be rescued by a compensatory mutation of the other...

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..We discuss implications for Structural Genomics initiatives and for improvements to sequence comparison methods...

..bantam microRNA simultaneously stimulates cell proliferation and prevents apoptosis. We identify the pro-apoptotic gene hid as a target for regulation by bantam miRNA, providing an explanation for bantam's anti-apoptotic activity...

..We conclude that the results from the intensively sampled ribosomal RNA genes supporting the Ecdysozoa hypothesis provide the most credible current estimates of metazoan phylogeny...

..Two examples (adenylate cyclase/DNA polymerase and glycogen phosphorylase/beta-glucosyltransferase) are presented to illustrate problems associated with protein classification...

..Since the method, SENSER, does not require knowledge of the three-dimensional structure, it can be used to infer relationships that are not tractable by methods dependent on structural templates...

..The presented data demonstrate a potential method for modulation of Src family kinase tyrosine phosphorylation through minor changes of the substrate SH3-interacting motif...

..For targets for which partial complexes are available, the speed and performance of the method make it an attractive complement to existing methods, as many different hypotheses can be tested quickly on a single processor...

..SuperTarget and Matador are available at http://insilico.charite.de/supertarget and http://matador.embl.de...

..Applying this approach to DNA damage signaling, we show that 53BP1 and Rad50 are phosphorylated by CDK1 and ATM, respectively. We describe a scalable strategy to evaluate predictions, which suggests that BCLAF1 is a GSK-3 substrate...

..The CASH domain is characterized by internal repetitions of glycines and hydrophobic residues that correspond to the repetitive units of a predicted or observed right-handed beta-helix structure of the pectate lyase superfamily...

..Structural details can ultimately turn abstract system representations into models that more accurately reflect biological reality...

..Overall therefore this mass spectrometry and homology modeling approach has given significant insight into the structure of two previously intractable protein complexes and as such has broad application in structural biology...

..A "systems" approach can help identify pathways related to a disease and can suggest secondary effects of drugs that might cause these problems and thus ultimately improve the drug discovery pipeline...