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2. Structural genomics is the largest contributor of novel structural leverage

Author

Nair, Rajesh, Liu, Jinfeng, Soong, Ta-Tsen, Acton, Thomas B, Everett, John K, Kouranov, Andrei, Fiser, Andras, Godzik, Adam, Jaroszewski, Lukasz, Orengo, Christine, Montelione, Gaetano T, and Rost, Burkhard

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Biotechnology, Human Genome, Computational Biology, Databases, Protein, Genomics, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Proteins, Proteomics, Environmental Sciences, Information and Computing Sciences, Biophysics, Biological sciences, Environmental sciences
Abstract

The Protein Structural Initiative (PSI) at the US National Institutes of Health (NIH) is funding four large-scale centers for structural genomics (SG). These centers systematically target many large families without structural coverage, as well as very large families with inadequate structural coverage. Here, we report a few simple metrics that demonstrate how successfully these efforts optimize structural coverage: while the PSI-2 (2005-now) contributed more than 8% of all structures deposited into the PDB, it contributed over 20% of all novel structures (i.e. structures for protein sequences with no structural representative in the PDB on the date of deposition). The structural coverage of the protein universe represented by today's UniProt (v12.8) has increased linearly from 1992 to 2008; structural genomics has contributed significantly to the maintenance of this growth rate. Success in increasing novel leverage (defined in Liu et al. in Nat Biotechnol 25:849-851, 2007) has resulted from systematic targeting of large families. PSI's per structure contribution to novel leverage was over 4-fold higher than that for non-PSI structural biology efforts during the past 8 years. If the success of the PSI continues, it may just take another approximately15 years to cover most sequences in the current UniProt database.

Published
2009

7. Demonstration of targeted crossovers in hybrid maize using CRISPR technology

Author

Vladimir Sidorov, Armstrong Charles L, Gasper Michelle Lee, Scott Huesgen, Timothy Boyle, Bryce Lemke, Ashok K. Shrawat, Richard J. Lawrence, Samuel Yang, and Kouranov Andrei Y

Subjects
Gene Editing, Agricultural genetics, DNA End-Joining Repair, QH301-705.5, Medicine (miscellaneous), Computational biology, Biology, Zea mays, General Biochemistry, Genetics and Molecular Biology, Chromosomes, Plant, Article, Plant breeding, CRISPR, Hybridization, Genetic, Crossing Over, Genetic, Biology (General), CRISPR-Cas Systems, General Agricultural and Biological Sciences
Abstract

Naturally occurring chromosomal crossovers (CO) during meiosis are a key driver of genetic diversity. The ability to target CO at specific allelic loci in hybrid plants would provide an advantage to the plant breeding process by facilitating trait introgression, and potentially increasing the rate of genetic gain. We present the first demonstration of targeted CO in hybrid maize utilizing the CRISPR Cas12a system. Our experiments showed that stable and heritable targeted CO can be produced in F1 somatic cells using Cas12a at a significantly higher rate than the natural CO in the same interval. Molecular characterization of the recombinant plants demonstrated that the targeted CO were driven by the non-homologous end joining (NHEJ) or HDR repair pathways, presumably during the mitotic cell cycle. These results are a step towards the use of RNA-guided nuclease technology to simplify the creation of targeted genome combinations in progeny and accelerate breeding., Kouranov et al. demonstrate Cas12a-mediated targeted chromosomal crossover (CO) in transgenic hybrid maize plants and produce heritable crossover in F1 plants when Cas12a transgene is segregated away. The authors also report that the frequency of LbCas12a-mediated CO is higher than control natural CO in the same intervals in the progeny of 4 different events.

Published
2021

11. The protein structure initiative structural genomics knowledgebase

Author

Berman, Helen M., Westbrook, John D., Gabanyi, Margaret J., Tao, Wendy, Shah, Raship, Kouranov, Andrei, Schwede, Torsten, Arnold, Konstantin, Kiefer, Florian, Bordoli, Lorenza, Kopp, Jürgen, Podvinec, Michael, Adams, Paul D., Carter, Lester G., Minor, Wladek, Nair, Rajesh, and Baer, Joshua La

Published
2009

16. A combined computational-experimental approach predicts human microRNA targets

Author

Kiriakidou, Marianthi, Nelson, Peter T., Kouranov, Andrei, Fitziev, Petko, Bouyioukos, Costas, Hatzigeorgiou, Atemis, and Mourelatos, Zissimos

Subjects
Computational biology -- Research, Mitochondria -- Research, RNA -- Research, Genetic research, Biological sciences
Abstract

A study was conducted using a combined bioinformatics and experimental approach to identity important rules governing miRNA-MRE recognition that allows prediction of human miRNA targets. A computational program 'DIANA-microT', that predicts mRNA targets for animal miRNAs and predicts mRNA targets, bearing single MREs, for human and mouse miRNAs is also developed.

Published
2004

17. The RCSB PDB information portal for structural genomics

Author

Lei Xie, John D. Westbrook, Joanna de la Cruz, Philip E. Bourne, Li Chen, Kouranov Andrei Y, and Helen M. Berman

Subjects
Genetics, Internet, Genome, Human, Protein Data Bank (RCSB PDB), Proteins, Genomics, computer.file_format, Computational biology, Biology, Protein Data Bank, Genome, Article, Structural genomics, User-Computer Interface, Protein structure, Structural Homology, Protein, Humans, natural sciences, Human genome, Databases, Protein, computer, Protein Structure Initiative
Abstract

The RCSB Protein Data Bank (PDB) offers online tools, summary reports and target information related to the worldwide structural genomics initiatives from its portal at http://sg.pdb.org. There are currently three components to this site: Structural Genomics Initiatives contains information and links on each structural genomics site, including progress reports, target lists, target status, targets in the PDB and level of sequence redundancy; Targets provides combined target information, protocols and other data associated with protein structure determination; and Structures offers an assessment of the progress of structural genomics based on the functional coverage of the human genome by PDB structures, structural genomics targets and homology models. Functional coverage can be examined according to enzyme classification, gene ontology (biological process, cell component and molecular function) and disease.

Published
2006
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18. The protein structure initiative structural genomics knowledgebase

Author

Berman, Helen M., Westbrook, John D., Gabanyi, Margaret J., Tao, Wendy, Shah, Raship, Kouranov, Andrei, Schwede, Torsten, Arnold, Konstantin, Kiefer, Florian, Bordoli, Lorenza, Kopp, Jürgen, Podvinec, Michael, Adams, Paul D., Carter, Lester G., Minor, Wladek, Nair, Rajesh, Baer, Joshua La, Berman, Helen M., Westbrook, John D., Gabanyi, Margaret J., Tao, Wendy, Shah, Raship, Kouranov, Andrei, Schwede, Torsten, Arnold, Konstantin, Kiefer, Florian, Bordoli, Lorenza, Kopp, Jürgen, Podvinec, Michael, Adams, Paul D., Carter, Lester G., Minor, Wladek, Nair, Rajesh, and Baer, Joshua La

Abstract

The Protein Structure Initiative Structural Genomics Knowledgebase (PSI SGKB, http://kb.psi-structuralgenomics.org) has been created to turn the products of the PSI structural genomics effort into knowledge that can be used by the biological research community to understand living systems and disease. This resource provides central access to structures in the Protein Data Bank (PDB), along with functional annotations, associated homology models, worldwide protein target tracking information, available protocols and the potential to obtain DNA materials for many of the targets. It also offers the ability to search all of the structural and methodological publications and the innovative technologies that were catalyzed by the PSI's high-throughput research efforts. In collaboration with the Nature Publishing Group, the PSI SGKB provides a research library, editorials about new research advances, news and an events calendar to present a broader view of structural biology and structural genomics. By making these resources freely available, the PSI SGKB serves as a bridge to connect the structural biology and the greater biomedical communities

Published
2017

19. Structural genomics is the largest contributor of novel structural leverage

Author

Lukasz Jaroszewski, Gaetano T. Montelione, Kouranov Andrei Y, Adam Godzik, Thomas Acton, Christine A. Orengo, Jinfeng Liu, Andras Fiser, John K. Everett, Burkhard Rost, Rajesh Nair, and Ta Tsen Soong

Subjects
Proteomics, Evolution, Computer science, Protein Conformation, Nuclear Magnetic Resonance, 030303 biophysics, Structural genomics, Protein Data Bank (RCSB PDB), Biophysics, Genomics, Biochemistry, Article, 03 medical and health sciences, Databases, Structural Biology, Information and Computing Sciences, Genetics, Leverage (statistics), Databases, Protein, Nuclear Magnetic Resonance, Biomolecular, 030304 developmental biology, 0303 health sciences, Protein, Human Genome, Proteins, Computational Biology, General Medicine, Biological Sciences, Data science, Protein structure determination, Structural biology, Protein universe, UniProt, Environmental Sciences, Biotechnology, Biomolecular
Abstract

The Protein Structural Initiative (PSI) at the US National Institutes of Health (NIH) is funding four large-scale centers for structural genomics (SG). These centers systematically target many large families without structural coverage, as well as very large families with inadequate structural coverage. Here, we report a few simple metrics that demonstrate how successfully these efforts optimize structural coverage: while the PSI-2 (2005-now) contributed more than 8% of all structures deposited into the PDB, it contributed over 20% of all novel structures (i.e. structures for protein sequences with no structural representative in the PDB on the date of deposition). The structural coverage of the protein universe represented by today's UniProt (v12.8) has increased linearly from 1992 to 2008; structural genomics has contributed significantly to the maintenance of this growth rate. Success in increasing novel leverage (defined in Liu et al. in Nat Biotechnol 25:849-851, 2007) has resulted from systematic targeting of large families. PSI's per structure contribution to novel leverage was over 4-fold higher than that for non-PSI structural biology efforts during the past 8 years. If the success of the PSI continues, it may just take another approximately15 years to cover most sequences in the current UniProt database.

Published
2009

20. The protein structure initiative structural genomics knowledgebase

Author

Michael Podvinec, Jürgen Kopp, Torsten Schwede, Margaret Gabanyi, Lorenza Bordoli, Lester G. Carter, Paul D. Adams, Joshua La Baer, Raship Shah, Rajesh Nair, Konstantin Arnold, Wladek Minor, Helen M. Berman, Florian Kiefer, Wendy Tao, Kouranov Andrei Y, and John D. Westbrook

Subjects
Engineering, Protein Conformation, 030303 biophysics, Protein Data Bank (RCSB PDB), Genomics, Computational biology, Biology, Bioinformatics, Biochemistry, Structural genomics, 03 medical and health sciences, 0302 clinical medicine, Genetics, Databases, Protein, Molecular Biology, 030304 developmental biology, 0303 health sciences, business.industry, Proteins, computer.file_format, Articles, Protein Data Bank, Data science, Living systems, Structural biology, Structural Homology, Protein, Protein target, business, computer, 030217 neurology & neurosurgery, Biotechnology, Protein Structure Initiative
Abstract

The Protein Structure Initiative Structural Genomics Knowledgebase (PSI SGKB, http://kb.psi-structuralgenomics.org) has been created to turn the products of the PSI structural genomics effort into knowledge that can be used by the biological research community to understand living systems and disease. This resource provides central access to structures in the Protein Data Bank (PDB), along with functional annotations, associated homology models, worldwide protein target tracking information, available protocols and the potential to obtain DNA materials for many of the targets. It also offers the ability to search all of the structural and methodological publications and the innovative technologies that were catalyzed by the PSI's high-throughput research efforts. In collaboration with the Nature Publishing Group, the PSI SGKB provides a research library, editorials about new research advances, news and an events calendar to present a broader view of structural biology and structural genomics. By making these resources freely available, the PSI SGKB serves as a bridge to connect the structural biology and the greater biomedical communities.

Published
2008

21. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Author

Hillier, LaDeana W, Miller, Webb, Birney, Ewan, Warren, Wesley, Hardison, Ross C, Ponting, Chris P, Bork, Peer, Burt, Peer, Groenen, Martien A M, Delany, Mary E, Dodgson, Jerry B, Chinwalla, Asif, Cliften, Paul F, Clifton, Sandra W, Delehaunty, Kimberly D, Fronick, Catrina, Fulton, Robert S, Graves, Tina A, Kremitzki, Colin, Layman, Dan, Magrini, Vincent, McPherson, John D, Miner, Tracie L, Minx, Patrick, Nash, William E, Nhan, Michael N, Nelson, Joanne O, Oddy, Lachlan G, Pohl, Craig S, Randall-Maher, Jennifer, Smith, Scott M, Wallis, John W, Yang, Shiaw-Pyng, Romanov, Michael N, Rondelli, Catherine M, Paton, Bob, Smith, Jacqueline, Morrice, David, Daniels, Laura, Tempest, Helen G, Robertson, Lindsay, Masabanda, Julio S, Griffin, Darren K., Vignal, Alain, Fillon, Valerie, Jacobbson, Lina, Kerje, Susanne, Andersson, Leif, Crooijmans, Richard P M A, Aerts, Jan, van der Poel, Jan J, Ellegren, Hans, Caldwell, Randolph B, Hubbard, Simon J, Grafham, Darren V, Kierzek, Andrzej M, McLaren, Stuart R, Overton, Ian M, Arakawa, Hiroshi, Beattie, Kevin J, Bezzubov, Yuri, Boardman, Paul E, Bonfield, James K, Croning, Michael D R, Davies, Robert M, Francis, Matthew D, Humphray, Sean J, Scott, Carol E, Taylor, Ruth G, Tickle, Cheryll, Brown, William R A, Rogers, Jane, Buerstedde, Jean-Marie, Wilson, Stuart A, Stubbs, Lisa, Ovcharenko, Ivan, Gordon, Laurie, Lucas, Susan, Miller, Marcia M, Inoko, Hidetoshi, Shiina, Takashi, Kaufman, Jim, Salomonsen, Jan, Skjoedt, Karsten, Wong, Gane Ka-Shu, Wang, Jun, Liu, Bin, Wang, Jian, Yu, Jun, Yang, Huanming, Nefedov, Mikhail, Koriabine, Maxim, de Jong, Pieter J, Goodstadt, Leo, Webber, Caleb, Dickens, Nicholas J, Letunic, Ivica, Suyama, Mikita, Torrents, David, von Mering, Christian, Zdobnov, Evgeny M, Makova, Kateryna, Nekrutenko, Anton, Elnitski, Laura, Eswara, Pallavi, King, David C, Yang, Shan, Tyekucheva, Svitlana, Radakrishnan, Anusha, Harris, Robert S, Chiaromonte, Francesca, Taylor, James, He, Jianbin, Rijnkels, Monique, Griffiths-Jones, Sam, Ureta-Vidal, Abe, Hoffman, Michael M, Severin, Jessica, Searle, Stephen M J, Law, Andy S, Speed, David, Waddington, David, Cheng, Ze, Tuzun, Eray, Eichler, Evan, Bao, Zhirong, Flicek, Paul, Shteynberg, David D, Brent, Michael R, Bye, Jacqueline M, Huckle, Elizabeth J, Chatterjee, Sourav, Dewey, Colin, Pachter, Lior, Kouranov, Andrei, Mourelatos, Zissimos, Hatzigeorgiou, Artemis G, Paterson, Andrew H, Ivarie, Robert, Brandstrom, Mikael, Axelsson, Erik, Backström, Niclas, Berlin, Sofia, Webster, Matthew T, Pourquie, Olivier, Reymond, Alexandre, Ucla, Catherine, Antonarakis, Stylianos E, Long, Manyuan, Emerson, J J, Betran, Esther, Dupanloup, Isabelle, Kaessmann, Henrik, Hinrichs, Angie S, Bejerano, Gill, Furey, Terrence S, Harte, Rachel A, Raney, Brian, Siepel, Adam, Kent, W James, Haussler, David, Eyras, Eduardo, Castelo, Robert, Abril, Josep F, Castellano, Sergi, Camara, Francisco, Parra, Genis, Guigo, Roderic, Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., Smit, Arian F. A., Fulton, Lucinda A., Mardis, Elaine R., Wilson, Richard K., International Chicken Genome Sequencing Consortium, ProdInra, Migration, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Zdobnov, Evgeny

Subjects
RNA, Untranslated, olfactory receptor, [SDV]Life Sciences [q-bio], mouse genome, QH75, Genome, 0302 clinical medicine, Gene Duplication, Coding region, ddc:576.5, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Short Interspersed Nucleotide Elements, Genetics, 0303 health sciences, Multidisciplinary, CHICKENS, recent segmental duplications, Untranslated, GENOME SEQUENCE, International Chicken Genome Sequencing Consortium, Genomics, Physical Chromosome Mapping, major histocompatibility complex, mammalian evolution, [SDV] Life Sciences [q-bio], Multigene Family, Vertebrates, SEQUENCE DU GENOME, Sequence Analysis, Pseudogenes, Biotechnology, brown-norway rat, animal structures, Evolution, General Science & Technology, Sequence analysis, Biology, Animal Breeding and Genomics, Synteny, Evolution, Molecular, Avian Proteins, 03 medical and health sciences, non-ltr retrotransposons, Animals, Humans, alcohol-dehydrogenase, Fokkerij en Genomica, SF, QP506, Gene, QH426, 030304 developmental biology, Whole genome sequencing, QL, phylogenetic analysis, QH, Human Genome, Molecular, Sequence Analysis, DNA, DNA, tissue-specific genes, EVOLUTION, Retroviridae, Long Interspersed Nucleotide Elements, Genes, Mutagenesis, Evolutionary biology, DNA Transposable Elements, Microchromosome, WIAS, RNA, Chickens, 030217 neurology & neurosurgery
Abstract

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Published
2004

22. Tic22 is targeted to the intermembrane space of chloroplasts by a novel pathway

Author

Danny J. Schnell, Huan Wang, and Kouranov Andrei Y

Subjects
Chloroplasts, Reticulocytes, Mitochondrial intermembrane space, medicine.disease_cause, Biochemistry, Chloroplast membrane, Adenosine Triphosphate, Protein targeting, medicine, Protein biosynthesis, Animals, Protein Precursors, Molecular Biology, Plant Proteins, biology, Membrane transport protein, Peas, Membrane Proteins, Membrane Transport Proteins, Cell Biology, Histone-Lysine N-Methyltransferase, Recombinant Proteins, Cell biology, Chloroplast, Membrane protein, Protein Biosynthesis, biology.protein, Rabbits, Intermembrane space, Carrier Proteins
Abstract

Tic22 previously was identified as a component of the general import machinery that functions in the import of nuclear-encoded proteins into the chloroplast. Tic22 is peripherally associated with the outer face of the inner chloroplast envelope membrane, making it the first known resident of the intermembrane space of the envelope. We have investigated the import of Tic22 into isolated chloroplasts to define the requirements for targeting of proteins to the intermembrane space. Tic22 is nuclear-endoded and synthesized as a preprotein with a 50-amino acid N-terminal presequence. The analysis of deletion mutants and chimerical proteins indicates that the precursor of Tic22 (preTic22) presequence is necessary and sufficient for targeting to the intermembrane space. Import of preTic22 was stimulated by ATP and required the presence of protease-sensitive components on the chloroplast surface. PreTic22 import was not competed by an excess of an authentic stromal preprotein, indicating that targeting to the intermembrane space does not involve the general import pathway utilized by stromal preproteins. On the basis of these observations, we conclude that preTic22 is targeted to the intermembrane space of chloroplasts by a novel import pathway that is distinct from known pathways that target proteins to other chloroplast subcompartments.

Published
1999

23. Protein translocation at the envelope and thylakoid membranes of chloroplasts

Author

Kouranov Andrei Y and Danny J. Schnell

Subjects
Chloroplasts, Chemistry, Chlamydomonas, Membrane Proteins, Biological Transport, Cell Biology, Protein Sorting Signals, Biochemistry, Models, Biological, Cytochromes f, Twin-arginine translocation pathway, Chloroplast, Thylakoid, Biophysics, Animals, Cytochromes, Protein translocation, Molecular Biology, Envelope (waves), Plant Proteins
Published
1996

24. Erratum: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Author

Hillier, LaDeana W, Miller, Webb, Birney, Ewan, Warren, Wesley, Hardison, Ross C, Ponting, Chris P, Bork, Peer, Burt, Peer, Groenen, Martien A M, Delany, Mary E, Dodgson, Jerry B, Chinwalla, Asif, Cliften, Paul F, Clifton, Sandra W, Delehaunty, Kimberly D, Fronick, Catrina, Fulton, Robert S, Graves, Tina A, Kremitzki, Colin, Layman, Dan, Magrini, Vincent, McPherson, John D, Miner, Tracie L, Minx, Patrick, Nash, William E, Nhan, Michael N, Nelson, Joanne O, Oddy, Lachlan G, Pohl, Craig S, Randall-Maher, Jennifer, Smith, Scott M, Wallis, John W, Yang, Shiaw-Pyng, Romanov, Michael N, Rondelli, Catherine M, Paton, Bob, Smith, Jacqueline, Morrice, David, Daniels, Laura, Tempest, Helen G, Robertson, Lindsay, Masabanda, Julio S, Griffin, Darren K., Vignal, Alain, Fillon, Valerie, Jacobbson, Lina, Kerje, Susanne, Andersson, Leif, Crooijmans, Richard P M A, Aerts, Jan, van der Poel, Jan J, Ellegren, Hans, Caldwell, Randolph B, Hubbard, Simon J, Grafham, Darren V, Kierzek, Andrzej M, McLaren, Stuart R, Overton, Ian M, Arakawa, Hiroshi, Beattie, Kevin J, Bezzubov, Yuri, Boardman, Paul E, Bonfield, James K, Croning, Michael D R, Davies, Robert M, Francis, Matthew D, Humphray, Sean J, Scott, Carol E, Taylor, Ruth G, Tickle, Cheryll, Brown, William R A, Rogers, Jane, Buerstedde, Jean-Marie, Wilson, Stuart A, Stubbs, Lisa, Ovcharenko, Ivan, Gordon, Laurie, Lucas, Susan, Miller, Marcia M, Inoko, Hidetoshi, Shiina, Takashi, Kaufman, Jim, Salomonsen, Jan, Skjoedt, Karsten, Wong, Gane Ka-Shu, Wang, Jun, Liu, Bin, Wang, Jian, Yu, Jun, Yang, Huanming, Nefedov, Mikhail, Koriabine, Maxim, de Jong, Pieter J, Goodstadt, Leo, Webber, Caleb, Dickens, Nicholas J, Letunic, Ivica, Suyama, Mikita, Torrents, David, von Mering, Christian, Zdobnov, Evgeny M, Makova, Kateryna, Nekrutenko, Anton, Elnitski, Laura, Eswara, Pallavi, King, David C, Yang, Shan, Tyekucheva, Svitlana, Radakrishnan, Anusha, Harris, Robert S, Chiaromonte, Francesca, Taylor, James, He, Jianbin, Rijnkels, Monique, Griffiths-Jones, Sam, Ureta-Vidal, Abe, Hoffman, Michael M, Severin, Jessica, Searle, Stephen M J, Law, Andy S, Speed, David, Waddington, David, Cheng, Ze, Tuzun, Eray, Eichler, Evan, Bao, Zhirong, Flicek, Paul, Shteynberg, David D, Brent, Michael R, Bye, Jacqueline M, Huckle, Elizabeth J, Chatterjee, Sourav, Dewey, Colin, Pachter, Lior, Kouranov, Andrei, Mourelatos, Zissimos, Hatzigeorgiou, Artemis G, Paterson, Andrew H, Ivarie, Robert, Brandstrom, Mikael, Axelsson, Erik, Backström, Niclas, Berlin, Sofia, Webster, Matthew T, Pourquie, Olivier, Reymond, Alexandre, Ucla, Catherine, Antonarakis, Stylianos E, Long, Manyuan, Emerson, J J, Betran, Esther, Dupanloup, Isabelle, Kaessmann, Henrik, Hinrichs, Angie S, Bejerano, Gill, Furey, Terrence S, Harte, Rachel A, Raney, Brian, Siepel, Adam, Kent, W James, Haussler, David, Eyras, Eduardo, Castelo, Robert, Abril, Josep F, Castellano, Sergi, Camara, Francisco, Parra, Genis, Guigo, Roderic, Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., Smit, Arian F. A., Fulton, Lucinda A., Mardis, Elaine R., Wilson, Richard K., Hillier, LaDeana W, Miller, Webb, Birney, Ewan, Warren, Wesley, Hardison, Ross C, Ponting, Chris P, Bork, Peer, Burt, Peer, Groenen, Martien A M, Delany, Mary E, Dodgson, Jerry B, Chinwalla, Asif, Cliften, Paul F, Clifton, Sandra W, Delehaunty, Kimberly D, Fronick, Catrina, Fulton, Robert S, Graves, Tina A, Kremitzki, Colin, Layman, Dan, Magrini, Vincent, McPherson, John D, Miner, Tracie L, Minx, Patrick, Nash, William E, Nhan, Michael N, Nelson, Joanne O, Oddy, Lachlan G, Pohl, Craig S, Randall-Maher, Jennifer, Smith, Scott M, Wallis, John W, Yang, Shiaw-Pyng, Romanov, Michael N, Rondelli, Catherine M, Paton, Bob, Smith, Jacqueline, Morrice, David, Daniels, Laura, Tempest, Helen G, Robertson, Lindsay, Masabanda, Julio S, Griffin, Darren K., Vignal, Alain, Fillon, Valerie, Jacobbson, Lina, Kerje, Susanne, Andersson, Leif, Crooijmans, Richard P M A, Aerts, Jan, van der Poel, Jan J, Ellegren, Hans, Caldwell, Randolph B, Hubbard, Simon J, Grafham, Darren V, Kierzek, Andrzej M, McLaren, Stuart R, Overton, Ian M, Arakawa, Hiroshi, Beattie, Kevin J, Bezzubov, Yuri, Boardman, Paul E, Bonfield, James K, Croning, Michael D R, Davies, Robert M, Francis, Matthew D, Humphray, Sean J, Scott, Carol E, Taylor, Ruth G, Tickle, Cheryll, Brown, William R A, Rogers, Jane, Buerstedde, Jean-Marie, Wilson, Stuart A, Stubbs, Lisa, Ovcharenko, Ivan, Gordon, Laurie, Lucas, Susan, Miller, Marcia M, Inoko, Hidetoshi, Shiina, Takashi, Kaufman, Jim, Salomonsen, Jan, Skjoedt, Karsten, Wong, Gane Ka-Shu, Wang, Jun, Liu, Bin, Wang, Jian, Yu, Jun, Yang, Huanming, Nefedov, Mikhail, Koriabine, Maxim, de Jong, Pieter J, Goodstadt, Leo, Webber, Caleb, Dickens, Nicholas J, Letunic, Ivica, Suyama, Mikita, Torrents, David, von Mering, Christian, Zdobnov, Evgeny M, Makova, Kateryna, Nekrutenko, Anton, Elnitski, Laura, Eswara, Pallavi, King, David C, Yang, Shan, Tyekucheva, Svitlana, Radakrishnan, Anusha, Harris, Robert S, Chiaromonte, Francesca, Taylor, James, He, Jianbin, Rijnkels, Monique, Griffiths-Jones, Sam, Ureta-Vidal, Abe, Hoffman, Michael M, Severin, Jessica, Searle, Stephen M J, Law, Andy S, Speed, David, Waddington, David, Cheng, Ze, Tuzun, Eray, Eichler, Evan, Bao, Zhirong, Flicek, Paul, Shteynberg, David D, Brent, Michael R, Bye, Jacqueline M, Huckle, Elizabeth J, Chatterjee, Sourav, Dewey, Colin, Pachter, Lior, Kouranov, Andrei, Mourelatos, Zissimos, Hatzigeorgiou, Artemis G, Paterson, Andrew H, Ivarie, Robert, Brandstrom, Mikael, Axelsson, Erik, Backström, Niclas, Berlin, Sofia, Webster, Matthew T, Pourquie, Olivier, Reymond, Alexandre, Ucla, Catherine, Antonarakis, Stylianos E, Long, Manyuan, Emerson, J J, Betran, Esther, Dupanloup, Isabelle, Kaessmann, Henrik, Hinrichs, Angie S, Bejerano, Gill, Furey, Terrence S, Harte, Rachel A, Raney, Brian, Siepel, Adam, Kent, W James, Haussler, David, Eyras, Eduardo, Castelo, Robert, Abril, Josep F, Castellano, Sergi, Camara, Francisco, Parra, Genis, Guigo, Roderic, Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., Smit, Arian F. A., Fulton, Lucinda A., Mardis, Elaine R., and Wilson, Richard K.

Abstract

International Chicken Genome Sequencing Consortium. The Original Article was published on 09 December 2004. Nature432, 695–716 (2004). In Table 5 of this Article, the last four values listed in the ‘Copy number’ column were incorrect. These should be: LTR elements, 30,000; DNA transposons, 20,000; simple repeats, 140,000; and satellites, 4,000. These errors do not affect any of the conclusions in our paper. Additional information. The online version of the original article can be found at 10.1038/nature03154

Published
2005

25. Molecular dissection of the mechanism of protein import into chloroplasts

Author

Danny J. Schnell, Kouranov Andrei Y, S.E. LaSala, F. Tian, and Y. Ma

Subjects
Chloroplasts, Chemistry, Recombinant Fusion Proteins, Ribulose-Bisphosphate Carboxylase, Biological Transport, Active, Membrane Proteins, Dissection (medical), In Vitro Techniques, medicine.disease, Biochemistry, Models, Biological, Cell biology, Chloroplast, Adenosine Triphosphate, Immunoglobulin G, Botany, Genetics, medicine, Guanosine Triphosphate, Protein Precursors, Staphylococcal Protein A, Molecular Biology, Mechanism (sociology), Plant Proteins
Published
1995

26. How to use the PSI Structural Genomics Knowledgebase to Enable Research

Author

Kouranov, Andrei, primary, Westbrook, John, additional, Gabanyi, Margaret, additional, Tao, Yi-Ping, additional, Shah, Raship, additional, Schwede, Torsten, additional, Arnold, Konstantin, additional, Kiefer, Florian, additional, Bordoli, Lorenza, additional, Adams, Paul, additional, Carter, Lester, additional, Minor, Wladek, additional, Nair, Rajesh, additional, LaBaer, Joshua, additional, and Berman, Helen M., additional

Published
2010
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27. The Protein Structure Initiative Structural Genomics Knowledgebase

Author

Gabanyi, Margaret, primary, Westbrook, John, additional, Tao, Wendy, additional, Shah, Raship, additional, Kouranov, Andrei, additional, Schwede, Torsten, additional, Arnold, Konstantin, additional, Kiefer, Florian, additional, Bordoli, Lorenza, additional, Podvinec, Michael, additional, Kopp, Jurgen, additional, Adams, Paul, additional, Carter, Lester, additional, Minor, Wladek, additional, Nair, Rajesh, additional, La Baer, Joshua, additional, and Berman, Helen M., additional

Published
2009
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28. The PSI structural genomics knowledgebase

Author

Kouranov Andrei Y, Paul D. Adams, John D. Westbrook, W. Tao, Helen M. Berman, Torsten Schwede, Rajesh Nair, and Raship Shah

Subjects
Engineering, Structural Biology, business.industry, Computational biology, business, Structural genomics
Published
2008
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30. Two Components of the Chloroplast Protein Import Apparatus,IAP86 and IAP75, Interact with the Transit Sequence during theRecognition and Translocation of Precursor Proteins at the OuterEnvelope.

Author

Yongkang Ma, Gordon C., Kouranov, Andrei, LaSala, Samuel E., and Schnell, Danny J.

Subjects
*PROTEIN precursors, *CHLOROPLASTS, *PROTEIN crosslinking, *ADENOSINE triphosphate, *HYDROLYSIS
Abstract

Focuses on the investigation for interactions of precursorproteins with components of the chloroplast envelope during theearly stages of protein import using a chemical cross-linkingstrategy. Components of the outer envelope import machinery;Concentration of adenosine triphosphate hydrolysis in the stromalcompartment; General stages of protein import across thechloroplast envelope.

Published
1996

31. The protein structure initiative structural genomics knowledgebase

Author

Berman, Helen M., Westbrook, John D., Gabanyi, Margaret J., Tao, Wendy, Shah, Raship, Kouranov, Andrei, Schwede, Torsten, Arnold, Konstantin, Kiefer, Florian, Bordoli, Lorenza, Kopp, Jürgen, Podvinec, Michael, Adams, Paul D., Carter, Lester G., Minor, Wladek, Nair, Rajesh, Baer, Joshua La, Berman, Helen M., Westbrook, John D., Gabanyi, Margaret J., Tao, Wendy, Shah, Raship, Kouranov, Andrei, Schwede, Torsten, Arnold, Konstantin, Kiefer, Florian, Bordoli, Lorenza, Kopp, Jürgen, Podvinec, Michael, Adams, Paul D., Carter, Lester G., Minor, Wladek, Nair, Rajesh, and Baer, Joshua La

Abstract

The Protein Structure Initiative Structural Genomics Knowledgebase (PSI SGKB, http://kb.psi-structuralgenomics.org) has been created to turn the products of the PSI structural genomics effort into knowledge that can be used by the biological research community to understand living systems and disease. This resource provides central access to structures in the Protein Data Bank (PDB), along with functional annotations, associated homology models, worldwide protein target tracking information, available protocols and the potential to obtain DNA materials for many of the targets. It also offers the ability to search all of the structural and methodological publications and the innovative technologies that were catalyzed by the PSI's high-throughput research efforts. In collaboration with the Nature Publishing Group, the PSI SGKB provides a research library, editorials about new research advances, news and an events calendar to present a broader view of structural biology and structural genomics. By making these resources freely available, the PSI SGKB serves as a bridge to connect the structural biology and the greater biomedical communities

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