Journal: Nucleic Acids Research

Volume 30, Issue 13

2727 -- 2735Perry M. Kim, Kimberly S. Paffett, Jachen A. Solinger, Wolf-Dietrich Heyer, Jac A. Nickoloff. Spontaneous and double-strand break-induced recombination, and gene conversion tract lengths, are differentially affected by overexpression of wild-type or ATPase-defective yeast Rad54
2736 -- 2741Duyen T. Dang, Weidong Zhao, Channing S. Mahatan, Deborah E. Geiman, Vincent W. Yang. Opposing effects of Krüppel-like factor 4 (gut-enriched Krüppel-like factor) and Krüppel-like factor 5 (intestinal-enriched Krüppel-like factor) on the promoter of the Krüppel-like factor 4 gene
2742 -- 2750Li Liu, Shuqiu Cheng, Anja J. van Brabant, Eric B. Kmiec. Rad51p and Rad54p, but not Rad52p, elevate gene repair in Saccharomyces cerevisiae directed by modified single-stranded oligonucleotide vectors
2751 -- 2757Dorte Renneberg, Emilie Bouliong, Ulrich Reber, Daniel Schümperli, Christian J. Leumann. Antisense properties of tricyclo-DNA
2758 -- 2763Liya Gu, Jianxin Wu, Bei-Bei Zhu, Guo-Min Li. Deficiency of a novel mismatch repair activity in a bladder tumor cell line
2764 -- 2771Andreas W. Rüfer, Brian Sauer. Non-contact positions impose site selectivity on Cre recombinase
2782 -- 2789Christopher J. Nulf, David R. Corey. DNA assembly using bis-peptide nucleic acids (bisPNAs)
2790 -- 2799Melanie P. Gygi, Mark D. Ferguson, Heather C. Mefford, Kevin P. Lund, Christine O Day, Peiwen Zhou, Cynthia Friedman, Ger van den Engh, Mark L. Stolowitz, Barbara J. Trask. Use of fluorescent sequence-specific polyamides to discriminate human chromosomes by microscopy and flow cytometry
2800 -- 2808Alexandros G. Georgakilas, Paula V. Bennett, Betsy M. Sutherland. High efficiency detection of bi-stranded abasic clusters in -irradiated DNA by putrescine
2809 -- 2816Esther E. Biswas, Pei-Hua Chen, Subhasis B. Biswas. Modulation of enzymatic activities of Escherichia coli DnaB helicase by single-stranded DNA-binding proteins
2817 -- 2824Maria A. Graziewicz, Brian J. Day, William C. Copeland. The mitochondrial DNA polymerase as a target of oxidative damage
2825 -- 2831Mark P. McPike, Julie M. Sullivan, Jerry Goodisman, James C. Dabrowiak. Footprinting, circular dichroism and UV melting studies on neomycin B binding to the packaging region of human immunodeficiency virus type-1 RNA
2832 -- 2843Ioannis Amarantos, Ioannis K. Zarkadis, Dimitrios L. Kalpaxis. The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions
2844 -- 2850Christine Mayer, Uttam L. RajBhandary. Conformational change of Escherichia coli initiator methionyl-tRNAfMet upon binding to methionyl-tRNA formyl transferase
2851 -- 2861Kazuko Shiroki, Chieko Ohsawa, Natuki Sugi, Motoaki Wakiyama, Kin-ichiro Miura, Manabu Watanabe, Yutaka Suzuki, Sumio Sugano. Internal ribosome entry site-mediated translation of Smad5 in vivo: requirement for a nuclear event
2862 -- 2870Chao Wei, Rose Skopp, Minoru Takata, Shunichi Takeda, Carolyn M. Price. Effects of double-strand break repair proteins on vertebrate telomere structure
2871 -- 2876Cristian Cañestro, Roser Gonzàlez-Duarte, Ricard Albalat. Minisatellite instability at the Adh locus reveals somatic polymorphism in amphioxus
2877 -- 2885Patrick J. Finn, Lei Sun, Satyam Nampalli, Haiguang Xiao, John R. Nelson, J. Anthony Mamone, Greg Grossmann, Parke K. Flick, Carl W. Fuller, Shiv Kumar. Synthesis and application of charge-modified dye-labeled dideoxynucleoside-5 -triphosphates to ?direct-load? DNA sequencing
2886 -- 2893Chiara Sabatti, Lars Rohlin, Min-Kyu Oh, James C. Liao. Co-expression pattern from DNA microarray experiments as a tool for operon prediction
2894 -- 2898Kristyna Stehlikova, Hana Kostrhunova, Jana Kasparkova, Viktor Brabec. DNA bending and unwinding due to the major 1, 2-GG intrastrand cross-link formed by antitumor cis-diamminedichloroplatinum(II) are flanking-base independent
2899 -- 2905Imre Cserpán, Róbert Katona, Tünde Praznovszky, Edit Novák, Márta Rózsavölgyi, Erika Csonka, Mónika Mórocz, Katalin Fodor, Gyula Hadlaczky. The chAB4 and NF1-related long-range multisequence DNA families are contiguous in the centromeric heterochromatin of several human chromosomes
2906 -- 2910Ippeita Dan, Norinobu M. Watanabe, Eriko Kajikawa, Takafumi Ishida, Akhilesh Pandey, Akihiro Kusumi. Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution
2920 -- 2929Kerby Shedden, Stephen Cooper. Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods
2930 -- 2939Ying Chen, Rajiv P. Sharma, Robert H. Costa, Erminio Costa, Dennis R. Grayson. On the epigenetic regulation of the human reelin promoter
2940 -- 2949Subhra Chakraborty, Bhaskarjyoti Sarmah, Niranjan Chakraborty, Asis Datta. Premature termination of RNA polymerase II mediated transcription of a seed protein gene in Schizosaccharomyces pombe
2950 -- 2960Franca Fraternali, Luigi Cavallo. Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome
2961 -- 2971Yi Zhang, Zhijie Li, Daniel S. Pilch, Michael J. Leibowitz. Pentamidine inhibits catalytic activity of group I intron Ca.LSU by altering RNA folding
2972 -- 2979Luciano De Haro, Ralf Janknecht. Functional analysis of the transcription factor ER71 and its activation of the matrix metalloproteinase-1 promoter
2980 -- 2986Torunn Berge, Nigel S. Jenkins, Richard B. Hopkirk, Michael J. Waring, J. Michael Edwardson, Robert M. Henderson. Structural perturbations in DNA caused by bis-intercalation of ditercalinium visualised by atomic force microscopy
2987 -- 2994Guillaume Achaz, Eduardo P. C. Rocha, P. Netter, Eric Coissac. Origin and fate of repeats in bacteria
2995 -- 3004Conchita Vens, Els Dahmen-Mooren, Manon Verwijs-Janssen, Wim Blyweert, Lise Graversen, Harry Bartelink, Adrian C. Begg. The role of DNA polymerase beta in determining sensitivity to ionizing radiation in human tumor cells
3005 -- 3014Jun Chen, Liang Ren Zhang, Ji Mei Min, Li He Zhang. Studies on the synthesis of a G-rich octaoligoisonucleotide (isoT)2(isoG)4(isoT)2 by the phosphotriester approach and its formation of G-quartet structure

Volume 30, Issue 1

1 -- 12Andreas D. Baxevanis. The Molecular Biology Database Collection: 2002 update
13 -- 16David L. Wheeler, Deanna M. Church, Alex E. Lash, Detlef D. Leipe, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Tatiana A. Tatusova, Lukas Wagner, Barbara A. Rapp. Database resources of the National Center for Biotechnology Information: 2002 update
17 -- 20Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Barbara A. Rapp, David L. Wheeler. GenBank
21 -- 26Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Evelyn Camon, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Nicole Redaschi, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan. The EMBL Nucleotide Sequence Database
27 -- 30Yoshio Tateno, Tadashi Imanishi, Satoru Miyazaki, Kaoru Fukami-Kobayashi, Naruya Saitou, Hideaki Sugawara, Takashi Gojobori. DNA Data Bank of Japan (DDBJ) for genome scale research in life science
31 -- 34Hans-Werner Mewes, Dmitrij Frishman, Ulrich Güldener, Gertrud Mannhaupt, Klaus F. X. Mayer, Martin Mokrejs, Burkhard Morgenstern, Martin Münsterkötter, Stephen Rudd, B. Weil. MIPS: a database for genomes and protein sequences
35 -- 37Cathy H. Wu, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhang-Zhi Hu, Robert S. Ledley, Kali C. Lewis, Hans-Werner Mewes, Bruce C. Orcutt, Baris E. Suzek, Akira Tsugita, C. R. Vinayaka, Lai-Su L. Yeh, Jian Zhang, Winona C. Barker. The Protein Information Resource: an integrated public resource of functional annotation of proteins
38 -- 41Tim J. P. Hubbard, Daniel Barker, Ewan Birney, Graham Cameron, Yuan Chen, Laura Clarke, Tony Cox, James A. Cuff, Val Curwen, Thomas Down, Richard Durbin, Eduardo Eyras, James Gilbert, Martin Hammond, Lukasz Huminiecki, Arek Kasprzyk, Heikki Lehväslaiho, Philip Lijnzaad, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Matthew R. Pocock, Simon C. Potter, Alastair Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, Michele E. Clamp. The Ensembl genome database project
42 -- 46Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Akihiro Nakaya. The KEGG databases at GenomeNet
47 -- 49Ida Schomburg, Antje Chang, Dietmar Schomburg. BRENDA, enzyme data and metabolic information
50 -- 51Björn M. Ursing, Frank H. J. van Enckevort, Jack A. M. Leunissen, Roland J. Siezen. EXProt: a database for proteins with an experimentally verified function
52 -- 55Ada Hamosh, Alan F. Scott, Joanna S. Amberger, Carol A. Bocchini, David Valle, Victor A. McKusick. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
56 -- 58Peter D. Karp, Monica Riley, Milton H. Saier Jr., Ian T. Paulsen, Julio Collado-Vides, Suzanne M. Paley, Alida Pellegrini-Toole, César Bonavides-Martínez, Socorro Gama-Castro. The EcoCyc Database
59 -- 61Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole. The MetaCyc Database
62 -- 65Ivan Moszer, Louis M. Jones, Sandrine Moreira, Cécilia Fabry, Antoine Danchin. SubtiList: the reference database for the Bacillus subtilis genome
66 -- 68Masaki Fumoto, Satoru Miyazaki, Hideaki Sugawara. Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more
69 -- 72Selina S. Dwight, Midori A. Harris, Kara Dolinski, Catherine A. Ball, Gail Binkley, Karen R. Christie, Dianna G. Fisk, Laurie Issel-Tarver, Mark Schroeder, Gavin Sherlock, Anand Sethuraman, Shuai Weng, David Botstein, J. Michael Cherry. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
73 -- 75Anuj Kumar, Kei-Hoi Cheung, Nick P. Tosches, Peter Masiar, Yang Liu, Perry L. Miller, Michael Snyder. The TRIPLES database: a community resource for yeast molecular biology
76 -- 79Stéphane Le Crom, Frédéric Devaux, Claude Jacq, Philippe Marc. yMGV: helping biologists with yeast microarray data mining
80 -- 83Georg Habeler, Klaus Natter, Gerhard G. Thallinger, Matthew E. Crawford, Sepp D. Kohlwein, Zlatko Trajanoski. YPL.db: the Yeast Protein Localization database
84 -- 86Lisa Kreppel, Alan R. Kimmel. Genomic database resources for Dictyostelium discoideum
87 -- 90Amit Bahl, Brian P. Brunk, Ross L. Coppel, Jonathan Crabtree, Sharon J. Diskin, Martin J. Fraunholz, Gregory R. Grant, Dinesh Gupta, Robert L. Huestis, Jessica C. Kissinger, Philip Labo, Li Li, Shannon K. McWeeney, Arthur J. Milgram, David S. Roos, Jonathan Schug, Christian J. Stoeckert Jr.. PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)
91 -- 93Heiko Schoof, Paolo Zaccaria, Heidrun Gundlach, Kai Lemcke, Stephen Rudd, Grigory Kolesov, Roland Arnold, Hans-Werner Mewes, Klaus F. X. Mayer. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome
94 -- 97Franck Samson, Véronique Brunaud, Sandrine Balzergue, B. Dubreucq, L. Lepiniec, G. Pelletier, Michel Caboche, Alain Lecharny. FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants
98 -- 102Katsumi Sakata, Yoshiaki Nagamura, Hisataka Numa, Baltazar A. Antonio, Hideki Nagasaki, Atsuko Idonuma, Wakako Watanabe, Yuji Shimizu, Ikuo Horiuchi, Takashi Matsumoto, Takuji Sasaki, Kenichi Higo. RiceGAAS: an automated annotation system and database for rice genome sequence
103 -- 105Doreen Ware, Pankaj Jaiswal, Junjian Ni, Xiaokang Pan, Kuan Chang, Kenneth Clark, Leonid Teytelman, Steven Schmidt, Wei Zhao, Samuel Cartinhour, Susan McCouch, Lincoln Stein. Gramene: a resource for comparative grass genomics
109 -- 112Yves Van de Peer, John Shawe-Taylor, Jayabalan Joseph, Axel Meyer. Wanda: a database of duplicated fish genes
113 -- 115Judith A. Blake, Joel E. Richardson, Carol J. Bult, James A. Kadin, Janan T. Eppig. The Mouse Genome Database (MGD): the model organism database for the laboratory mouse
116 -- 118Hidemasa Bono, Takeya Kasukawa, Masaaki Furuno, Yoshihide Hayashizaki, Yasushi Okazaki. FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones
119 -- 120Takeshi Kawashima, Shuichi Kawashima, Yuji Kohara, Minoru Kanehisa, Kazuhiro W. Makabe. Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags
121 -- 124Stanton L. Martin, Barbara P. Blackmon, Ravi Rajagopalan, Thomas D. Houfek, Robert G. Sceeles, Sheila O. Denn, Thomas K. Mitchell, Douglas E. Brown, Rod A. Wing, Ralph A. Dean. MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea
125 -- 128Simon N. Twigger, Jian Lu, Mary Shimoyama, Dan Chen, Dean Pasko, Hanping Long, Jessica Ginster, Chin-Fu Chen, Rajni Nigam, Anne E. Kwitek, Janan T. Eppig, Lois Maltais, Donna R. Maglott, Gregory D. Schuler, Howard J. Jacob, Peter J. Tonellato. Rat Genome Database (RGD): mapping disease onto the genome
129 -- 136Anthony Kerlavage, Vivien Bonazzi, Matteo di Tommaso, Charles Lawrence, Peter Li, Frank Mayberry, Richard J. Mural, Marc Nodell, Mark Yandell, Jinghui Zhang, Paul Thomas. The Celera Discovery SystemTM
137 -- 141Peter E. Hodges, Pauline M. Carrico, Jennifer D. Hogan, Kathy E. O Neill, J. J. Owen, Mary Mangan, Brian P. Davis, Joan E. Brooks, James I. Garrels. Annotating the human proteome: the Human Proteome Survey Database (HumanPSDTM) and an in-depth target database for G protein-coupled receptors (GPCR-PDTM) from Incyte Genomics
142 -- 144Claude-Alain H. Roten, Patrick Gamba, Jean-Luc Barblan, Dimitri Karamata. Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes
145 -- 148Donald G. Gilbert. euGenes: a eukaryote genome information system
149 -- 151Samson Chien, Lawrence T. Reiter, Ethan Bier, Michael Gribskov. Homophila: human disease gene cognates in Drosophila
152 -- 157Mika Hirakawa. HOWDY: an integrated database system for human genome research
158 -- 162Mika Hirakawa, Toshihiro Tanaka, Yoichi Hashimoto, Masako Kuroda, Toshihisa Takagi, Yusuke Nakamura. JSNP: a database of common gene variations in the Japanese population
163 -- 165Micheal Hewett, Diane E. Oliver, Daniel L. Rubin, Katrina L. Easton, Joshua M. Stuart, Russ B. Altman, Teri E. Klein. PharmGKB: the Pharmacogenetics Knowledge Base
166 -- 168Reiko Kikuno, Takahiro Nagase, Mina Waki, Osamu Ohara. HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project
169 -- 171Hester M. Wain, Michael J. Lush, Fabrice Ducluzeau, Sue Povey. Genew: the Human Gene Nomenclature Database
172 -- 173Marcella Attimonelli, Domenico Catalano, Carmela Gissi, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Monica Santamaria, Graziano Pesole, Cecilia Saccone. MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002
174 -- 175Cecilia Lanave, Flavio Licciulli, Mariateresa De Robertis, Alessandra Marolla, Marcella Attimonelli. Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences
176 -- 178Maciej Szymanski, Miroslawa Z. Barciszewska, Volker A. Erdmann, Jan Barciszewski. 5S Ribosomal RNA Database
179 -- 182Kelly P. Williams. The tmRNA Website: invasion by an intron
183 -- 185Jan Wuyts, Yves Van de Peer, Tina Winkelmans, Rupert De Wachter. The European database on small subunit ribosomal RNA
186 -- 190Y.-H. Huang, Y. T. Chen, J.-J. Lai, S.-T. Yang, U.-C. Yang. PALS db: Putative Alternative Splicing database
191 -- 194Meena K. Sakharkar, F. Passetti, J. E. de Souza, Manyuan Long, Sandro J. de Souza. ExInt: an Exon Intron Database
195 -- 199Julia V. Ponomarenko, Galina Orlova, Anatoly S. Frolov, Mikhail S. Gelfand, Mikhail P. Ponomarenko. SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data
200 -- 202Vadim P. Valuev, Dmitry A. Afonnikov, Mikhail P. Ponomarenko, Luciano Milanesi, Nikolay A. Kolchanov. ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro
203 -- 204Kenji Onodera, Ulrich Melcher. VirOligo: a database of virus-specific oligonucleotides
205 -- 206Jan Paces, Adam Pavlícek, Václav Paces. HERVd: database of human endogenous retroviruses
207 -- 210Ron Edgar, Michael Domrachev, Alex E. Lash. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
211 -- 213Hidemasa Bono, Takeya Kasukawa, Yoshihide Hayashizaki, Yasushi Okazaki. READ: RIKEN Expression Array Database
214 -- 217Peter M. Haverty, Zhiping Weng, Nathan L. Best, Kenneth R. Auerbach, Li-Li Hsiao, Roderick V. Jensen, Steven R. Gullans. HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues
218 -- 220Peter S. Nelson, Colin C. Pritchard, Denise Abbott, Nigel Clegg. The human (PEDB) and mouse (mPEDB) Prostate Expression Databases
221 -- 225Toshihiko Honkura, Jun Ogasawara, Tomoyuki Yamada, Shinichi Morishita. The Gene Resource Locator: gene locus maps for transcriptome analysis
226 -- 229Christian Schönbach, Judice L. Y. Koh, Darren R. Flower, Limsoon Wong, Vladimir Brusic. FIMM, a database of functional molecular immunology: update 2002
230 -- 231Jean-Marie Buerstedde, Hiroshi Arakawa, Akira Watahiki, Piero Carninci, Yoshihide Hayashizaki, Bernhard Korn, Jiri Plachy. The DT40 web site: sampling and connecting the genes of a B cell line
232 -- 234Jouni Väliaho, Marianne Pusa, Tuomo Ylinen, Mauno Vihinen. IDR: the ImmunoDeficiency Resource
235 -- 238Laurent Falquet, Marco Pagni, Philipp Bucher, Nicolas Hulo, Christian J. A. Sigrist, Kay Hofmann, Amos Bairoch. The PROSITE database, its status in 2002
239 -- 241Terri K. Attwood, Martin J. Blythe, Darren R. Flower, Anna Gaulton, J. E. Mabey, Neil Maudling, L. McGregor, Alex Mitchell, G. Moulton, K. Paine, Philip Scordis. PRINTS and PRINTS-S shed light on protein ancestry
242 -- 244Ivica Letunic, Leo Goodstadt, Nicholas J. Dickens, Tobias Doerks, Jörg Schultz, Richard Mott, Francesca Ciccarelli, Richard R. Copley, Chris P. Ponting, Peer Bork. Recent improvements to the SMART domain-based sequence annotation resource
245 -- 248John D. Westbrook, Zukang Feng, Shri Jain, T. N. Bhat, Narmada Thanki, Veerasamy Ravichandran, Gary Gilliland, Wolfgang Bluhm, Helge Weissig, Douglas S. Greer, Philip E. Bourne, Helen M. Berman. The Protein Data Bank: unifying the archive
249 -- 252Yanli Wang, John B. Anderson, Jie Chen, Lewis Y. Geer, Siqian He, David I. Hurwitz, Cynthia A. Liebert, Thomas Madej, Gabriele H. Marchler, Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Stephen H. Bryant. MMDB: Entrez s 3D-structure database
253 -- 254Jan Reichert, Jürgen Sühnel. The IMB Jena Image Library of Biological Macromolecules: 2002 update
255 -- 259Ursula Pieper, Narayanan Eswar, Ashley C. Stuart, Valentin A. Ilyin, Andrej Sali. MODBASE, a database of annotated comparative protein structure models
260 -- 263John-Marc Chandonia, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, Steven E. Brenner. ASTRAL compendium enhancements
264 -- 267Loredana Lo Conte, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin. SCOP database in 2002: refinements accommodate structural genomics
268 -- 272Julian Gough, Cyrus Chothia. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
273 -- 275Kristian Vlahovicek, János Murvai, Endre Barta, Sándor Pongor. The SBASE protein domain library, release 9.0: an online resource for protein domain identification
276 -- 280Alex Bateman, Ewan Birney, Lorenzo Cerutti, Richard Durbin, Laurence Ettwiller, Sean R. Eddy, Sam Griffiths-Jones, Kevin L. Howe, Mhairi Marshall, Erik L. L. Sonnhammer. The Pfam Protein Families Database
281 -- 283Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, Paul A. Thiessen, Lewis Y. Geer, Stephen H. Bryant. CDD: a database of conserved domain alignments with links to domain three-dimensional structure
284 -- 288V. Mallika, Anirban Bhaduri, Ramanathan Sowdhamini. PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies
289 -- 293Shashi B. Pandit, Dilip Gosar, S. Abhiman, S. Sujatha, Sayali S. Dixit, Natasha S. Mhatre, Ramanathan Sowdhamini, Narayanaswamy Srinivasan. SUPFAM - a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes
294 -- 298Takeshi Kawabata, Satoshi Fukuchi, Keiichi Homma, Motonori Ota, Jiro Araki, Takehiko Ito, Nobuyuki Ichiyoshi, Ken Nishikawa. GTOP: a database of protein structures predicted from genome sequences
299 -- 300Antje Krause, Stefan A. Haas, Eivind Coward, Martin Vingron. SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein
301 -- 302M. Michael Gromiha, Hatsuho Uedaira, Jianghong An, Samuel Selvaraj, Ponraj Prabakaran, Akinori Sarai. ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0
303 -- 305Ioannis Xenarios, Lukasz Salwínski, Xiaoqun Joyce Duan, Patrick Higney, Sul-Min Kim, David Eisenberg. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
306 -- 309Joseph C. Mellor, Itai Yanai, Karl H. Clodfelter, Julian Mintseris, Charles DeLisi. Predictome: a database of putative functional links between proteins
310 -- 311Grant H. Jacobs, Oliver Rackham, Peter A. Stockwell, Warren Tate, Chris M. Brown. Transterm: a database of mRNAs and translational control elements
312 -- 317Nikolay A. Kolchanov, Elena V. Ignatieva, Elena A. Ananko, Olga A. Podkolodnaya, Irina L. Stepanenko, Tatyana I. Merkulova, Mikhail A. Pozdnyakov, Nikolay L. Podkolodny, Andrey N. Naumochkin, Aida G. Romashchenko. Transcription Regulatory Regions Database (TRRD): its status in 2002
318 -- 321Raquel Tobes, Juan L. Ramos. AraC-XylS database: a family of positive transcriptional regulators in bacteria
322 -- 324Viviane Praz, Rouaïda Périer, Claude Bonnard, Philipp Bucher. The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data
325 -- 327Magali Lescot, Patrice Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouzé, Stephane Rombauts. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
328 -- 331Yutaka Suzuki, Riu Yamashita, Kenta Nakai, Sumio Sugano. DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
332 -- 334Olga V. Kel-Margoulis, Alexander E. Kel, Ingmar Reuter, Igor Deineko, Edgar Wingender. TRANSCompel®: a database on composite regulatory elements in eukaryotic genes
335 -- 340Graziano Pesole, Sabino Liuni, Giorgio Grillo, Flavio Licciulli, Flavio Mignone, Carmela Gissi, Cecilia Saccone. UTRdb and UTRsite: specialized databases of sequences and functional elements of 5 and 3 untranslated regions of eukaryotic mRNAs. Update 2002
341 -- 342Steven A. Sullivan, Daniel W. Sink, Kenneth L. Trout, Izabela Makalowska, Patrick M. Taylor, Andreas D. Baxevanis, David Landsman. The Histone Database
343 -- 346Neil D. Rawlings, Emmet A. O Brien, Alan J. Barrett. MEROPS: the protease database
347 -- 348F. De Leo, Mariateresa Volpicella, Flavio Licciulli, Sabino Liuni, Raffaele Gallerani, Luigi R. Ceci. PLANT-PIs: a database for plant protease inhibitors and their genes
349 -- 350Natalia Maltsev, E. Marland, G. X. Yu, S. Bhatnagar, R. Lusk. Sentra, a database of signal transduction proteins
351 -- 353Alexander V. Spirov, Mikhail Borovsky, Olesya A. Spirova. HOX Pro DB: the functional genomics of hox ensembles
354 -- 360Chiquito J. Crasto, Luis N. Marenco, Perry L. Miller, Gordon M. Shepherd. Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences
361 -- 363Øyvind Edvardsen, Anne Lise Reiersen, Margot W. Beukers, Kurt Kristiansen. tGRAP, the G-protein coupled receptors mutant database
364 -- 368Jorge Duarte, Guy Perrière, Vincent Laudet, Marc Robinson-Rechavi. NUREBASE: database of nuclear hormone receptors
369 -- 371Tae-Kwon Sohn, Eun-Joung Moon, Seok-Ki Lee, Hwan-Gue Cho, Kyu-Won Kim. AngioDB: database of angiogenesis and angiogenesis-related molecules
372 -- 374Ines Liebich, Jürgen Bode, Matthias Frisch, Edgar Wingender. S/MARt DB: a database on scaffold/matrix attached regions
375 -- 378Michael H. W. Weber, Ingo Fricke, Niclas Doll, Mohamed A. Marahiel. CSDBase: an interactive database for cold shock domain-containing proteins and the bacterial cold shock response
379 -- 382Jesus M. Castagnetto, Sean W. Hennessy, Victoria A. Roberts, Elizabeth D. Getzoff, John A. Tainer, Michael E. Pique. MDB: the Metalloprotein Database and Browser at The Scripps Research Institute
383 -- 384Francine B. Perler. InBase: the Intein Database
385 -- 386Fei Li, David L. Herrin. FUGOID: functional genomics of organellar introns database
387 -- 391D. Fredman, Marianne Siegfried, Yan P. Yuan, Peer Bork, Heikki Lehväslaiho, Anthony J. Brookes. HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources
392 -- 394Peter S. Klosterman, Makio Tamura, Stephen R. Holbrook, Steven E. Brenner. SCOR: a Structural Classification of RNA database
395 -- 397Uma Nagaswamy, Maia Larios-Sanz, James Hury, Shakaala Collins, Zhengdong Zhang, Qin Zhao, George E. Fox. NCIR: a database of non-canonical interactions in known RNA structures
398 -- 401Elena A. Ananko, Nikolay L. Podkolodny, Irina L. Stepanenko, Elena V. Ignatieva, Olga A. Podkolodnaya, Nikolay A. Kolchanov. GeneNet: a database on structure and functional organisation of gene networks
402 -- 404Susumu Goto, Yasushi Okuno, Masahiro Hattori, Takaaki Nishioka, Minoru Kanehisa. LIGAND: database of chemical compounds and reactions in biological pathways
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