Search

Your search keyword '"Rychlewski, Leszek"' showing total 508 results
Start Over Author "Rychlewski, Leszek"
508 results on '"Rychlewski, Leszek"'

3. The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes

Author

Bowler, Chris, Allen, Andrew E., Badger, Jonathan H., Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, Otillar, Robert P., Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Frederic, Berges, John A., Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Choi, Chang Jae, Coesel, Sacha, Martino, Alessandra De, Detter, J. Chris, Durkin, Colleen, Falciatore, Angela, Fournet, Jerome, Haruta, Miyoshi, Huysman, Marie, Jenkins, Bethany D., Jiroutova, Katerina, Jorgensen, Richard E., Joubert, Yolaine, Kaplan, Aaron, Kroeger, Nils, Kroth, Peter, Roche, Julie La, Lindquist, Erica, Lommer, Markus, Martin-Jezequel, Veronique, Lopez, Pascal J., Lucas, Susan, Mangogna, Manuela, McGinnis, Karen, Medlin, Linda K., Montsant, Anton, Secq, Marie-Pierre Oudot-Le, Napoli, Carolyn, Obornik, Miroslav, Petit, Jean-Louis, Porcel, Betina M., Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, Rynearson, Tatiana A., Schmutz, Jeremy, Parker, Micaela Schnitzler, Shapiro, Harris, Siaut, Magali, Stanley, Michele, Sussman, Michael J., Taylor, Alison, Vardi, Assaf, Dassow, Peter von, Vyverman, Wim, Willis, Anusuya, Wyrwicz, Lucjan S., Rokhsar, Daniel S., Weissenbach, Jean, Armbrust, E. Virginia, Green, Beverley R., Peer, Yves Van de, and Grigoriev, Igor V.

Subjects
Phaeodactylum genome, diatom genomes
Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (40percent) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Published
2008

4. FFAS03: a server for profile–profile sequence alignments

Author

Jaroszewski, Lukasz, Rychlewski, Leszek, Li, Zhanwen, Li, Weizhong, and Godzik, Adam

Subjects
Networking and Information Technology R&D (NITRD), Generic health relevance, Algorithms, Databases, Protein, Internet, Protein Folding, Sequence Alignment, Sequence Homology, Amino Acid, Software, User-Computer Interface, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

The FFAS03 server provides a web interface to the third generation of the profile-profile alignment and fold-recognition algorithm of fold and function assignment system (FFAS) [L. Rychlewski, L. Jaroszewski, W. Li and A. Godzik (2000), Protein Sci., 9, 232-241]. Profile-profile algorithms use information present in sequences of homologous proteins to amplify the patterns defining the family. As a result, they enable detection of remote homologies beyond the reach of other methods. FFAS, initially developed in 2000, is consistently one of the best ranked fold prediction methods in the CAFASP and LiveBench competitions. It is also used by several fold-recognition consensus methods and meta-servers. The FFAS03 server accepts a user supplied protein sequence and automatically generates a profile, which is then compared with several sets of sequence profiles of proteins from PDB, COG, PFAM and SCOP. The profile databases used by the server are automatically updated with the latest structural and sequence information. The server provides access to the alignment analysis, multiple alignment, and comparative modeling tools. Access to the server is open for both academic and commercial researchers. The FFAS03 server is available at http://ffas.burnham.org.

Published
2005

5. Practical lessons from protein structure prediction

Author

Ginalski, Krzysztof, Grishin, Nick V, Godzik, Adam, and Rychlewski, Leszek

Subjects
Biotechnology, Genetics, Human Genome, Underpinning research, 1.4 Methodologies and measurements, Generic health relevance, Algorithms, Computational Biology, Models, Molecular, Protein Conformation, Protein Folding, Sequence Analysis, Protein, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

Despite recent efforts to develop automated protein structure determination protocols, structural genomics projects are slow in generating fold assignments for complete proteomes, and spatial structures remain unknown for many protein families. Alternative cheap and fast methods to assign folds using prediction algorithms continue to provide valuable structural information for many proteins. The development of high-quality prediction methods has been boosted in the last years by objective community-wide assessment experiments. This paper gives an overview of the currently available practical approaches to protein structure prediction capable of generating accurate fold assignment. Recent advances in assessment of the prediction quality are also discussed.

Published
2005

6. Integrated web service for improving alignment quality based on segments comparison.

Author

Plewczynski, Dariusz, Rychlewski, Leszek, Ye, Yuzhen, Jaroszewski, Lukasz, and Godzik, Adam

Subjects
Peptide Fragments, Predictive Value of Tests, Sequence Alignment, Computational Biology, Internet, Software, Databases, Protein, Online Systems, Databases, Protein, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundDefining blocks forming the global protein structure on the basis of local structural regularity is a very fruitful idea, extensively used in description, and prediction of structure from only sequence information. Over many years the secondary structure elements were used as available building blocks with great success. Specially prepared sets of possible structural motifs can be used to describe similarity between very distant, non-homologous proteins. The reason for utilizing the structural information in the description of proteins is straightforward. Structural comparison is able to detect approximately twice as many distant relationships as sequence comparison at the same error rate.ResultsHere we provide a new fragment library for Local Structure Segment (LSS) prediction called FRAGlib which is integrated with a previously described segment alignment algorithm SEA. A joined FRAGlib/SEA server provides easy access to both algorithms, allowing a one stop alignment service using a novel approach to protein sequence alignment based on a network matching approach. The FRAGlib used as secondary structure prediction achieves only 73% accuracy in Q3 measure, but when combined with the SEA alignment, it achieves a significant improvement in pairwise sequence alignment quality, as compared to previous SEA implementation and other public alignment algorithms. The FRAGlib algorithm takes approximately 2 min. to search over FRAGlib database for a typical query protein with 500 residues. The SEA service align two typical proteins within circa approximately 5 min. All supplementary materials (detailed results of all the benchmarks, the list of test proteins and the whole fragments library) are available for download on-line at http://ffas.ljcrf.edu/darman/results/.ConclusionsThe joined FRAGlib/SEA server will be a valuable tool both for molecular biologists working on protein sequence analysis and for bioinformaticians developing computational methods of structure prediction and alignment of proteins.

Published
2004

17. BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases

Author

Ginalski, Krzysztof, Kinch, Lisa, Rychlewski, Leszek, and Grishin, Nick V.

Subjects
Adenosine triphosphate -- Research, Transglutaminases -- Research, Cysteine proteinases -- Research, Biological sciences, Chemistry
Abstract

Using sequence similarity searches and top-of-the-range fold-recognition methods, we have identified a novel family of bacterial transglutaminase-like cysteine proteinases (BTLCPs) with an invariant Cys-His-Asp catalytic triad and a predicted N-terminal signal sequence. This family of previously uncharacterized hypothetical proteins encompasses sequences of unknown function from DUF920 (in the Pfam database) and COG3672. BTLCPs are predicted to possess the papain-like cysteine proteinase fold and catalyze post-translational protein modification through transamidase, acetylase or hydrolase activity. Inspection of neighboring genes encoding BTLCPs suggests a link between this predicted activity and a type-I secretion system resembling ATP-binding cassette exporters of toxins and proteases involved in bacterial pathogenicity.

Published
2004

18. DCC proteins: a novel family of thiol-disulfide oxidoreductases

Author

Ginalski, Krzysztof, Kinch, Lisa, Rychlewski, Leszek, and Grishin, Nick V.

Subjects
Thioredoxin -- Usage, Protein research -- Evaluation, Biological sciences, Chemistry
Abstract

Using top-of-the-range fold-recognition methods, we have assigned a thioredoxin-like structure to a family of previously uncharacterized hypothetical proteins of bacterial origin. The DCC family, named after the conserved N-terminal DxxCxxC motif, encompasses proteins of unknown function from DUF393 (in Pfam database) and COG3011. The presence of two invariant potentially catalytic cysteine residues indicates that DCC proteins function as thiol-disulfide oxidoreductases.

Published
2004

22. Influenza Mutation from Equine to Canine

Author

Von Grotthuss, Marcin, Rychlewski, Leszek, Crawford, Patti C., Dubovi, Edward J., Castleman, William L., Stephenson, Iain, Gibbs, E. P. J., Chen, Limei, Smith, Catherine, Hill, Richard C., Ferro, Pamela, Pompey, Justine, Bright, Rick A., Medina, Marie-Jo, Johnson, Calvin M., Olsen, Christopher W., Cox, Nancy J., Klimov, Alexander I., Katz, Jackie M., and Donis, Ruben O.

Published
2006

25. ELM: the status of the 2010 eukaryotic linear motif resource

Author

Gould, Cathryn M., Diella, Francesca, Via, Allegra, Puntervoll, Pål, Gemünd, Christine, Chabanis-Davidson, Sophie, Michael, Sushama, Sayadi, Ahmed, Bryne, Jan Christian, Chica, Claudia, Seiler, Markus, Davey, Norman E., Haslam, Niall, Weatheritt, Robert J., Budd, Aidan, Hughes, Tim, Paś, Jakub, Rychlewski, Leszek, Travé, Gilles, Aasland, Rein, Helmer-Citterich, Manuela, Linding, Rune, and Gibson, Toby J.

Published
2010
Full Text
View/download PDF

26. Predicting Protein Structures Accurately

Author

von Grotthuss, Marcin, Wyrwicz, Lucjan S., Pas, Jakub, Rychlewski, Leszek, Bradley, Phil, Kuhlman, Brian, Dantas, Gautam, and Baker, David

Published
2004

29. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, Chris, Allen, Andrew E., Badger, Jonathan H., Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, Otillar, Robert P., Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Fréderic, Berges, John A., Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Choi, Chang Jae, Coesel, Sacha, De Martino, Alessandra, Detter, J. Chris, Durkin, Colleen, Falciatore, Angela, Fournet, Jérome, Haruta, Miyoshi, Huysman, Marie J. J., Jenkins, Bethany D., Jiroutova, Katerina, Jorgensen, Richard E., Joubert, Yolaine, Kaplan, Aaron, Kröger, Nils, Kroth, Peter G., La Roche, Julie, Lindquist, Erica, Lommer, Markus, Martin-Jézéquel, Véronique, Lopez, Pascal J., Lucas, Susan, Mangogna, Manuela, McGinnis, Karen, Medlin, Linda K., Montsant, Anton, Secq, Marie-Pierre Oudot-Le, Napoli, Carolyn, Obornik, Miroslav, Parker, Micaela Schnitzler, Petit, Jean-Louis, Porcel, Betina M., Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, Rynearson, Tatiana A., Schmutz, Jeremy, Shapiro, Harris, Siaut, Magali, Stanley, Michele, Sussman, Michael R., Taylor, Alison R., Vardi, Assaf, von Dassow, Peter, Vyverman, Wim, Willis, Anusuya, Wyrwicz, Lucjan S., Rokhsar, Daniel S., Weissenbach, Jean, Armbrust, E. Virginia, Green, Beverley R., Van de Peer, Yves, and Grigoriev, Igor V.

Published
2008
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results