Wed, 20 Aug 2008 21:16:02 BST CiteULike: marcius's Berman http://www.citeulike.org/user/marcius/author/Berman CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/marcius/article/1378982 <i>Nucleic Acids Res, Vol. 32, No. 5. (2004), pp. 1666-1677.</i><br /><br />RNA exhibits a large diversity of conformations. Three thousand nucleotides of 23S and 5S ribosomal RNA from a structure of the large ribosomal subunit were analyzed in order to classify their conformations. Fourier averaging of the six 3D distributions of torsion angles and analyses of the resulting pseudo electron maps, followed by clustering of the preferred combinations of torsion angles were performed on this dataset. Eighteen non-A-type conformations and 14 A-RNA related conformations were discovered and their torsion angles were determined; their Cartesian coordinates are available. RNA conformational classes. B Schneider Z Morávek HM Berman Nucleic Acids Res, Vol. 32, No. 5. (2004), pp. 1666-1677. 2007-06-11T16:56:41-00:00 2004 Nucleic Acids Res 1362-4962 32 5 1666 1677 biophysics classification rna rotamers http://www.citeulike.org/user/marcius/article/833683 <i>RNA, Vol. 12, No. 4. (April 2006), pp. 533-541.</i><br /><br />The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework-an RNA Ontology (RO)-with a common, dynamic, controlled, and structured vocabulary to describe and characterize RNA sequences, secondary structures, three-dimensional structures, and dynamics pertaining to RNA function. The RO should produce tools for clear communication about RNA structure and function for multiple uses, including the integration of RNA electronic resources into the Semantic Web. These tools should allow the accurate description in computer-interpretable form of the coupling between RNA architecture, function, and evolution. The purposes for creating the RO are, therefore, (1) to integrate sequence and structural databases; (2) to allow different computational tools to interoperate; (3) to create powerful software tools that bring advanced computational methods to the bench scientist; and (4) to facilitate precise searches for all relevant information pertaining to RNA. For example, one initial objective of the ROC is to define, identify, and classify RNA structural motifs described in the literature or appearing in databases and to agree on a computer-interpretable definition for each of these motifs. To achieve these aims, the ROC will foster communication and promote collaboration among RNA scientists by coordinating frequent face-to-face workshops to discuss, debate, and resolve difficult conceptual issues. These meeting opportunities will create new directions at various levels of RNA research. The ROC will work closely with the PDB/NDB structural databases and the Gene, Sequence, and Open Biomedical Ontology Consortia to integrate the RO with existing biological ontologies to extend existing content while maintaining interoperability. The RNA Ontology Consortium: an open invitation to the RNA community. NB Leontis RB Altman HM Berman SE Brenner JW Brown DR Engelke SC Harvey SR Holbrook F Jossinet SE Lewis F Major DH Mathews JS Richardson JR Williamson E Westhof doi:10.1261/rna.2343206 RNA, Vol. 12, No. 4. (April 2006), pp. 533-541. 2006-09-07T16:26:19-00:00 2006 RNA 1355-8382 12 4 533 541 bioinformatics classification clustering rna sequence structure http://www.citeulike.org/user/marcius/article/833679 <i>Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)</i><br /><br />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. The RCSB PDB information portal for structural genomics. A Kouranov L Xie J de la Cruz L Chen J Westbrook PE Bourne HM Berman Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006) 2006-09-07T16:21:13-00:00 2006 Nucleic Acids Res 1362-4962 34 Database issue databases protein_structure structural_genomics http://www.citeulike.org/user/marcius/article/275498 <i>Science, Vol. 309, No. 5736. (05 August 2005), pp. 938-940.</i><br /><br />Recent experiments revealed large-scale differences in the transcription programs of related species, yet little is known about the genetic basis underlying the evolution of gene expression and its contribution to phenotypic diversity. Here we describe a large-scale modulation of the yeast transcription program that is connected to the emergence of the capacity for rapid anaerobic growth. Genes coding for mitochondrial and cytoplasmic ribosomal proteins display a strongly correlated expression pattern in Candida albicans, but this correlation is lost in the fermentative yeast Saccharomyces cerevisiae. We provide evidence that this change in gene expression is connected to the loss of a specific cis-regulatory element from dozens of genes following the apparent whole-genome duplication event. Our results shed new light on the genetic mechanisms underlying the large-scale evolution of transcriptional networks. Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage Jan Ihmels Sven Bergmann Maryam Gerami-Nejad Itai Yanai Mark Mcclellan Judith Berman Naama Barkai doi:10.1126/science.1113833 Science, Vol. 309, No. 5736. (05 August 2005), pp. 938-940. 2005-08-05T18:55:10-00:00 2005 Science 309 5736 938 940 evolution gene_expression genes genome http://www.citeulike.org/user/marcius/article/447375 <i>Methods Biochem Anal, Vol. 44 (2003), pp. 41-73.</i> Fundamentals of DNA and RNA structure. S Neidle B Schneider HM Berman Methods Biochem Anal, Vol. 44 (2003), pp. 41-73. 2005-12-22T22:50:44-00:00 2003 Methods Biochem Anal 0076-6941 44 41 73 review rna structure http://www.citeulike.org/user/marcius/article/445762 <i>Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3450-3460.</i><br /><br />Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/. Tools for the automatic identification and classification of RNA base pairs Huanwang Yang Fabrice Jossinet Neocles Leontis Li Chen John Westbrook Helen Berman Eric Westhof Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3450-3460. 2005-12-21T00:37:45-00:00 2003 Nucl. Acids Res. 31 13 3450 3460 rna software structure