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Semantic ScholarNucleic Acids Research, Volume 40
Volume 40, Number Database-Issue, January 2012
- Michael Y. Galperin
, Xosé M. Fernández-Suárez:
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. 1-8 - Robert D. Finn, Paul P. Gardner, Alex Bateman:
Making your database available through Wikipedia: the pros and cons. 9-12 - Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Ian M. Fingerman, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, Sergey Krasnov, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Karsch-Mizrachi, James Ostell, Anna R. Panchenko, Lon Phan, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye:
Database resources of the National Center for Biotechnology Information. 13-25 - Igor V. Grigoriev, Henrik Nordberg, Igor Shabalov, Andrea Aerts, Mike Cantor, David M. Goodstein, Alan Kuo, Simon Minovitsky, Roman Nikitin, Robin A. Ohm, Robert Otillar, Alexander Poliakov, Igor Ratnere, Robert Riley, Tatyana Smirnova, Daniel Rokhsar, Inna Dubchak:
The Genome Portal of the Department of Energy Joint Genome Institute. 26-32 - Ilene Karsch-Mizrachi, Yasukazu Nakamura, Guy Cochrane:
The International Nucleotide Sequence Database Collaboration. 33-37 - Yuichi Kodama, Jun Mashima, Eli Kaminuma, Takashi Gojobori, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura:
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. 38-42 - Clara Amid, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Richard Gibson, Neil Goodgame, Christopher I. Hunter, Mikyung Jang, Rasko Leinonen, Xin Liu, Arnaud Oisel, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Stéphane Rivière, Marc Rossello, Alexander Senf, Dimitriy Smirnov, Petra ten Hoopen, Daniel Vaughan, Robert Vaughan, Vadim Zalunin, Guy Cochrane:
Major submissions tool developments at the European nucleotide archive. 43-47 - Dennis A. Benson, Ilene Karsch-Mizrachi, Karen Clark, David J. Lipman, James Ostell, Eric W. Sayers:
GenBank. 48-53 - Yuichi Kodama, Martin Shumway, Rasko Leinonen:
The sequence read archive: explosive growth of sequencing data. 54-56 - Tanya Barrett, Karen Clark, Robert Gevorgyan, Vyatcheslav Gorelenkov, Eugene Gribov, Ilene Karsch-Mizrachi, Michael Kimelman, Kim D. Pruitt, Sergei Resenchuk, Tatiana A. Tatusova, Eugene Yaschenko, James Ostell:
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. 57-63 - Mikhail Gostev, Adam Faulconbridge, Marco Brandizi, Julio Fernandez-Banet, Ugis Sarkans, Alvis Brazma, Helen E. Parkinson:
The BioSample Database (BioSD) at the European Bioinformatics Institute. 64-70 - Reorganizing the protein space at the Universal Protein Resource (UniProt). 71-75
- Lydie Lane, Ghislaine Argoud-Puy, Aurore Britan, Isabelle Cusin, Paula D. Duek, Olivier Evalet, Alain Gateau, Pascale Gaudet, Anne Gleizes, Alexandre Masselot, Catherine Zwahlen, Amos Bairoch:
neXtProt: a knowledge platform for human proteins. 76-83 - Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Monika Komorowska, Gautier Koscielny, Eugene Kulesha, Pontus Larsson, Ian Longden, William M. McLaren, Matthieu Muffato, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Harpreet Singh Riat, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Y. Amy Tang, Kieron R. Taylor, Stephen J. Trevanion, Jana Vandrovcova, Simon White, Mark Wilson, Steven P. Wilder, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suárez, Jennifer L. Harrow, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Giulietta Spudich, Jan Vogel, Andy Yates, Amonida Zadissa, Stephen M. J. Searle:
Ensembl 2012. 84-90 - Paul J. Kersey, Daniel M. Staines, Daniel Lawson, Eugene Kulesha, Paul S. Derwent, Jay C. Humphrey, Daniel S. T. Hughes, Stephen Keenan, Arnaud Kerhornou, Gautier Koscielny, Nicholas Langridge, Mark D. McDowall, Karine Megy, Uma Maheswari, Michael Nuhn, Michael Paulini, Helder Pedro, Iliana Toneva, Derek Wilson, Andrew D. Yates, Ewan Birney:
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. 91-97 - Flora J. Logan-Klumpler, Nishadi De Silva, Ulrike Böhme, Matthew B. Rogers, Giles Velarde, Jacqueline A. McQuillan, Tim Carver, Martin Aslett, Christian Olsen, Sandhya Subramanian, Isabelle Phan, Carol Farris, Siddhartha Mitra, Gowthaman Ramasamy, Haiming Wang, Adrian Tivey, Andrew Jackson, Robin Houston, Julian Parkhill, Matthew T. G. Holden, Omar S. Harb, Brian P. Brunk, Peter J. Myler, David S. Roos, Mark Carrington, Deborah F. Smith, Christiane Hertz-Fowler, Matthew Berriman:
GeneDB - an annotation database for pathogens. 98-108 - Minoru Kanehisa, Susumu Goto, Yoko Sato, Miho Furumichi, Mao Tanabe:
KEGG for integration and interpretation of large-scale molecular data sets. 109-114 - Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams, Marcel Huntemann, Iain Anderson, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
IMG: the integrated microbial genomes database and comparative analysis system. 115-122 - Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
IMG/M: the integrated metagenome data management and comparative analysis system. 123-129 - Kim D. Pruitt, Tatiana A. Tatusova, Garth R. Brown, Donna R. Maglott:
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. 130-135 - Scott Federhen:
The NCBI Taxonomy database. 136-143 - Hong-Mei Zhang, Hu Chen, Wei Liu, Hui Liu, Jing Gong, Huili Wang, An-Yuan Guo:
AnimalTFDB: a comprehensive animal transcription factor database. 144-149 - Riu Yamashita, Sumio Sugano, Yutaka Suzuki, Kenta Nakai:
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. 150-154 - Alberto Riva:
The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding sites. 155-161 - Aaron T. Spivak, Gary D. Stormo:
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. 162-168 - Carl G. de Boer, Timothy R. Hughes:
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. 169-179 - Gerd Anders, Sebastian D. Mackowiak, Marvin Jens, Jonas Maaskola, Andreas Kuntzagk, Nikolaus Rajewsky, Markus Landthaler, Christoph Dieterich:
doRiNA: a database of RNA interactions in post-transcriptional regulation. 180-186 - Manuel A. Candales, Adrian Duong, Keyar S. Hood, Tony Li, Ryan A. E. Neufeld, Runda Sun, Bonnie A. McNeil, Li Wu, Ashley M. Jarding, Steven Zimmerly:
Database for bacterial group II introns. 187-190 - Dawid Bielewicz, Jakub Dolata, Andrzej Zielezinski, Sylwia Alaba, Bogna Szarzynska, Michal W. Szczesniak, Artur Jarmolowski, Zofia Szweykowska-Kulinska, Wojciech M. Karlowski:
mirEX: a platform for comparative exploration of plant pri-miRNA expression data. 191-197 - Michal Wojciech Szczesniak, Sebastian Deorowicz, Jakub Gapski, Lukasz Kaczynski, Izabela Makalowska:
miRNEST database: an integrative approach in microRNA search and annotation. 198-204 - Alban Ott, Anouar Idali, Antonin Marchais, Daniel Gautheret:
NAPP: the Nucleic Acid Phylogenetic Profile Database. 205-209 - Dechao Bu, Kuntao Yu, Silong Sun, Chaoyong Xie, Geir Skogerbø, Ruoyu Miao, Hui Xiao, Qi Liao, Haitao Luo, Guoguang Zhao, Haitao Zhao, Zhiyong Liu, Changning Liu, Runsheng Chen, Yi Zhao:
NONCODE v3.0: integrative annotation of long noncoding RNAs. 210-215 - Jesse D. Ziebarth, Anindya Bhattacharya, Anlong Chen, Yan Cui:
PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits. 216-221 - Thanasis Vergoulis, Ioannis S. Vlachos, Panagiotis Alexiou, George Georgakilas, Manolis Maragkakis, Martin Reczko, Stefanos Gerangelos, Nectarios Koziris, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. 222-229 - Nishant Thakur, Abid Qureshi, Manoj Kumar:
VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. 230-236 - Ramana Madupu, Alexander R. Richter, Robert J. Dodson, Lauren M. Brinkac, Derek M. Harkins, A. Scott Durkin, Susmita Shrivastava, Granger G. Sutton, Daniel H. Haft:
CharProtDB: a database of experimentally characterized protein annotations. 237-241 - Holger Dinkel, Sushama Michael, Robert J. Weatheritt, Norman E. Davey, Kim Van Roey, Brigitte Altenberg, Grischa Toedt, Bora Uyar, Markus Seiler, Aidan Budd, Lisa Jödicke, Marcel A. Dammert, Christian Schroeter, Maria Hammer, Tobias Schmidt, Peter Jehl, Caroline McGuigan, Magdalena Dymecka, Claudia Chica, Katja Luck, Allegra Via, Andrew Chatr-aryamontri, Niall J. Haslam, Gleb Grebnev, Richard J. Edwards, Michel O. Steinmetz, Heike Meiselbach, Francesca Diella, Toby J. Gibson:
ELM - the database of eukaryotic linear motifs. 242-251 - Tian Mi, Jerlin Camilus Merlin, Sandeep Deverasetty, Michael R. Gryk, Travis J. Bill, Andrew W. Brooks, Logan Y. Lee, Viraj Rathnayake, Christian A. Ross, David P. Sargeant, Christy L. Strong, Paula Watts, Sanguthevar Rajasekaran, Martin R. Schiller:
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. 252-260 - Peter V. Hornbeck, Jon M. Kornhauser, Sasha Tkachev, Bin Zhang, Elzbieta Skrzypek, Beth Murray, Vaughan Latham, Michael Sullivan:
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. 261-270 - Jian Huang, Beibei Ru, Ping Zhu, Fulei Nie, Jun Yang, Xuyang Wang, Ping Dai, Hao Lin, Feng-Biao Guo, Nini Rao:
MimoDB 2.0: a mimotope database and beyond. 271-277 - Irina V. Medvedeva, Pavel Demenkov, Nikolay A. Kolchanov, Vladimir A. Ivanisenko:
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. 278-283 - Sean Powell, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Michael Kuhn, Jean Muller, Roland Arnold, Thomas Rattei, Ivica Letunic, Tobias Doerks, Lars Juhl Jensen, Christian von Mering, Peer Bork:
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. 284-289 - Marco Punta, Penny C. Coggill, Ruth Y. Eberhardt, Jaina Mistry, John G. Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn:
The Pfam protein families database. 290-301 - Ivica Letunic, Tobias Doerks, Peer Bork:
SMART 7: recent updates to the protein domain annotation resource. 302-305 - Sarah Hunter, Philip Jones, Alex L. Mitchell, Rolf Apweiler, Teresa K. Attwood, Alex Bateman, Thomas Bernard, David Binns, Peer Bork, Sarah W. Burge, Edouard De Castro, Penny C. Coggill, Matthew Corbett, Ujjwal Das, Louise Daugherty, Lauranne Duquenne, Robert D. Finn, Matthew Fraser, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Conor McMenamin, Huaiyu Mi, Prudence Mutowo-Meullenet, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Sebastien Pesseat, Marco Punta, Antony F. Quinn, Catherine Rivoire, Amaia Sangrador-Vegas, Jeremy D. Selengut, Christian J. A. Sigrist, Maxim Scheremetjew, John G. Tate, Manjulapramila Thimmajanarthanan, Paul D. Thomas, Cathy H. Wu, Corin Yeats, Siew-Yit Yong:
InterPro in 2011: new developments in the family and domain prediction database. 306-312 - Nadav Rappoport, Solange Karsenty, Amos Stern, Nathan Linial, Michal Linial:
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. 313-320 - Fanny Jadeau, Christophe Grangeasse, Lei Shi, Ivan Mijakovic, Gilbert Deléage, Christophe Combet:
BYKdb: the Bacterial protein tYrosine Kinase database. 321-324 - Quentin Kaas, Rilei Yu, Ai-Hua Jin, Sébastien Dutertre, David J. Craik:
ConoServer: updated content, knowledge, and discovery tools in the conopeptide database. 325-330 - Dongseop Kwon, Jong Hwan Yoon, Soo-Yong Shin, Tae-Ho Jang, Hong-Gee Kim, Insuk So, Ju-Hong Jeon, Hyun Ho Park:
A comprehensive manually curated protein-protein interaction database for the Death Domain superfamily. 331-336 - Satyajeet P. Khare, Farhat Habib, Rahul Sharma, Nikhil Gadewal, Sanjay Gupta, Sanjeev Galande:
HIstome - a relational knowledgebase of human histone proteins and histone modifying enzymes. 337-342 - Neil D. Rawlings, Alan J. Barrett, Alex Bateman:
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. 343-350 - Philipp F. Lange, Pitter F. Huesgen, Christopher M. Overall:
TopFIND 2.0 - linking protein termini with proteolytic processing and modifications altering protein function. 351-361 - Anjali Bansal Gupta, Ravi Kumar Verma, Vatsal Agarwal, Manu Vajpai, Vivek Bansal, Ramasubbu Sankararamakrishnan:
MIPModDB: a central resource for the superfamily of major intrinsic proteins. 362-369 - Mikhail A. Lomize, Irina D. Pogozheva, Hyeon Joo, Henry I. Mosberg, Andrei L. Lomize:
OPM database and PPM web server: resources for positioning of proteins in membranes. 370-376 - Bas Vroling, David Thorne, Philip McDermott, Henk-Jan Joosten, Teresa K. Attwood, Steve Pettifer, Gert Vriend:
NucleaRDB: information system for nuclear receptors. 377-380 - Bradley W. Langhorst, William E. Jack, Linda Reha-Krantz, Nicole M. Nichols:
Polbase: a repository of biochemical, genetic and structural information about DNA polymerases. 381-387 - Aadil H. Bhat, Homchoru Mondal, Jagat Singh Chauhan, Gajendra P. S. Raghava, Amrish Methi, Alka Rao:
ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins. 388-393 - Hong Luo, Ke Lin, Audrey David, Harm Nijveen, Jack A. M. Leunissen:
ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins. 394-399 - Yanli Wang, Jewen Xiao, Tugba O. Suzek, Jian Zhang, Jiyao Wang, Zhigang Zhou, Lianyi Han, Karen Karapetyan, Svetlana Dracheva, Benjamin A. Shoemaker, Evan Bolton, Asta Gindulyte, Stephen H. Bryant:
PubChem's BioAssay Database. 400-412 - Ayana Wiener, Marina Shudler, Anat Levit, Masha Y. Niv:
BitterDB: a database of bitter compounds. 413-419 - Saulius Grazulis, Adriana Daskevic, Andrius Merkys, Daniel Chateigner, Luca Lutterotti, Miguel Quirós, Nadezhda R. Serebryanaya, Peter Moeck, Robert T. Downs, Armel Le Bail:
Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration. 420-427 - Abraham Heifets, Igor Jurisica:
SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents. 428-433 - Joachim Schnabl, Pascal Suter, Roland K. O. Sigel:
MINAS - a database of Metal Ions in Nucleic AcidS. 434-438 - Pamela L. Vanegas, Graham A. Hudson, Amber R. Davis, Shannon C. Kelly, Charles C. Kirkpatrick, Brent M. Znosko:
RNA CoSSMos: Characterization of Secondary Structure Motifs - a searchable database of secondary structure motifs in RNA three-dimensional structures. 439-444 - Sameer Velankar, Younes Alhroub, Christoph Best, Ségolène Caboche, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Adel Golovin, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, E. Heuson, Miriam Hirshberg, Melford John, Ingvar C. Lagerstedt, Saqib Mir, Laurence E. Newman, Thomas J. Oldfield, Ardan Patwardhan, Luana Rinaldi, Gaurav Sahni, Eduardo Sanz-García, Sanchayita Sen, Robert A. Slowley, Antonio Suarez-Uruena, G. J. Swaminathan, Martyn F. Symmons, Wim F. Vranken, Michael E. Wainwright, Gerard J. Kleywegt:
PDBe: Protein Data Bank in Europe. 445-452 - Akira R. Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Daron M. Standley, Atsushi Nakagawa, Haruki Nakamura:
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. 453-460 - Thomas Madej, Kenneth J. Addess, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Christopher J. Lanczycki, Chunlei Liu, Shennan Lu, Aron Marchler-Bauer, Anna R. Panchenko, Jie Chen, Paul A. Thiessen, Yanli Wang, Dachuan Zhang, Stephen H. Bryant:
MMDB: 3D structures and macromolecular interactions. 461-464 - Jonathan G. Lees, Corin Yeats, James Richard Perkins, Ian Sillitoe, Robert Rentzsch, Benoit H. Dessailly, Christine A. Orengo:
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. 465-471 - Darby Tien-Hao Chang, Tsung-Ju Yao, Chen-Yu Fan, Chih-Yun Chiang, Yi-Han Bai:
AH-DB: collecting protein structure pairs before and after binding. 472-478 - Joan Segura, Baldomero Oliva, Narcis Fernandez-Fuentes:
CAPS-DB: a structural classification of helix-capping motifs. 479-485 - Harinder Singh, Jagat Singh Chauhan, M. Michael Gromiha, Gajendra P. S. Raghava:
ccPDB: compilation and creation of data sets from Protein Data Bank. 486-489 - Zong Hong Zhang, Kavitha Bharatham, Sharon M. Q. Chee, Ivana Mihalek:
Cube-DB: detection of functional divergence in human protein families. 490-494 - Alexander Jarasch, Philipp Dziuk, Thomas Becker, Jean-Paul Armache, Andreas Hauser, Daniel N. Wilson, Roland Beckmann:
The DARC site: a database of aligned ribosomal complexes. 495-500 - Xingyan Kuang, Jing Ginger Han, Nan Zhao, Bin Pang, Chi-Ren Shyu, Dmitry Korkin:
DOMMINO: a database of macromolecular interactions. 501-506 - Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Seiko D. Murakami, Takayuki Amemiya, Kazuo Hosoda, Ryotaro Koike, Hidekazu Hiroaki, Motonori Ota:
IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. 507-511 - Zheng Zhang, Cheng Xing, Lushan Wang, Bin Gong, Hui Liu:
IndelFR: a database of indels in protein structures and their flanking regions. 512-518 - Jurgen F. Doreleijers, Wim F. Vranken, Christopher F. Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend, Geerten W. Vuister:
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. 519-524 - Joshua SungWoo Yang, Ji-han Kim, Sangho Oh, Gukjeong Han, Sanghyuk Lee, Jinhyuk Lee:
STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures. 525-530 - Arumugam Gandhimathi, Anu G. Nair, Ramanathan Sowdhamini:
PASS2 version 4: An update to the database of structure-based sequence alignments of structural domain superfamilies. 531-534 - Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan:
Pocketome: an encyclopedia of small-molecule binding sites in 4D. 535-540 - Jun-Ichi Ito, Yasuo Tabei, Kana Shimizu, Koji Tsuda, Kentaro Tomii:
PoSSuM: a database of similar protein-ligand binding and putative pockets. 541-548 - Olga V. Kalinina, Oliver Wichmann, Gordana Apic, Robert B. Russell:
ProtChemSI: a network of protein-chemical structural interactions. 549-553 - Takayuki Amemiya, Ryotaro Koike, Akinori Kidera, Motonori Ota:
PSCDB: a database for protein structural change upon ligand binding. 554-558 - The Gene Ontology: enhancements for 2011. 559-564
- Emily C. Dimmer, Rachael P. Huntley, Yasmin Alam-Faruque, Tony Sawford, Claire O'Donovan, Maria Jesus Martin, Benoit Bely, Paul Browne, Wei Mun Chan, Ruth Y. Eberhardt, Michael Gardner, Kati Laiho, Duncan Legge, Michele Magrane, Klemens Pichler, Diego Poggioli, Harminder Sehra, Andrea H. Auchincloss, Kristian B. Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Silvia Braconi-Quintaje, Lionel Breuza, Alan Bridge, Elisabeth Coudert, Anne Estreicher, Maria Livia Famiglietti, Serenella Ferro-Rojas, Marc Feuermann, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Janet James, Silvia Jimenez, Florence Jungo, Guillaume Keller, Phillippe Lemercier, Damien Lieberherr, Patrick Masson, Madelaine Moinat, Ivo Pedruzzi, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Lydie Bougueleret, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek-Roggli, Ioannis Xenarios, Rolf Apweiler:
The UniProt-GO Annotation database in 2011. 565-570 - Ioanna Pagani, Konstantinos Liolios, Jakob Jansson, I-Min A. Chen, Tatyana Smirnova, Bahador Nosrat, Victor M. Markowitz, Nikos Kyrpides:
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. 571-579 - Nick S. Juty, Nicolas Le Novère, Camille Laibe:
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. 580-586 - Carla Kuiken, James Thurmond, Mira Dimitrijevic, Hyejin Yoon:
The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses. 587-592 - Brett E. Pickett, Eva L. Sadat, Yun Zhang, Jyothi Noronha, R. Burke Squires, Victoria Hunt, Mengya Liu, Sanjeev Kumar, Sam Zaremba, Zhiping Gu, Liwei Zhou, Christopher N. Larsen, Jonathan Dietrich, Edward B. Klem, Richard H. Scheuermann:
ViPR: an open bioinformatics database and analysis resource for virology research. 593-598 - Joseph A. Cruz, Yifeng Liu, Yongjie Liang, You Zhou, Michael Wilson, Jonathan J. Dennis, Paul Stothard, Gary H. Van Domselaar, David S. Wishart:
BacMap: an up-to-date electronic atlas of annotated bacterial genomes. 599-604 - Adam A. Witney, Denise E. Waldron, Lucy A. Brooks, Richard H. Tyler, Michael Withers, Neil G. Stoker, Brendan W. Wren, Philip D. Butcher, Jason Hinds:
BμG@Sbase - a microbial gene expression and comparative genomic database. 605-609 - Josch Pauling, Richard Röttger, Andreas Tauch, Vasco Azevedo, Jan Baumbach:
CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands. 610-614 - Abhijit Chakraborty, Sudeshna Ghosh, Garisha Chowdhary, Ujjwal Maulik, Saikat Chakrabarti:
DBETH: A Database of Bacterial Exotoxins for Human. 615-620 - Dexi Bi, Zhen Xu, Ewan M. Harrison, Cui Tai, Yiqing Wei, Xinyi He, Shiru Jia, Zixin Deng, Kumar Rajakumar, Hong-Yu Ou:
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. 621-626 - Blanca Taboada, Ricardo Ciria, Cristian E. Martinez-Guerrero, Enrique Merino:
ProOpDB: Prokaryotic Operon DataBase. 627-631 - Libusha Kelly, Katherine H. Huang, Huiming Ding, Sallie W. Chisholm:
ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage. 632-640 - Lihong Chen, Zhaohui Xiong, Lilian Sun, Jian Yang, Qi Jin:
VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. 641-645 - Patricia P. Chan, Andrew D. Holmes, Andrew M. Smith, Danny Tran, Todd M. Lowe:
The UCSC Archaeal Genome Browser: 2012 update. 646-652 - Martha B. Arnaud, Gustavo C. Cerqueira, Diane O. Inglis, Marek S. Skrzypek, Jonathan Binkley, Marcus C. Chibucos, Jonathan Crabtree, Clinton Howarth, Joshua Orvis, Prachi Shah, Farrell Wymore, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock, Jennifer R. Wortman:
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. 653-659 - Jane E. Mabey Gilsenan, John Cooley, Paul Bowyer:
CADRE: the Central Aspergillus Data REpository 2012. 660-666 - Diane O. Inglis, Martha B. Arnaud, Jonathan Binkley, Prachi Shah, Marek S. Skrzypek, Farrell Wymore, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock:
The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. 667-674 - Jason E. Stajich, Todd W. Harris, Brian P. Brunk, John Brestelli, Steve Fischer, Omar S. Harb, Jessica C. Kissinger, Wei Li, Vishal Nayak, Deborah F. Pinney, Christian J. Stoeckert Jr., David S. Roos:
FungiDB: an integrated functional genomics database for fungi. 675-681 - Cheuk C. Siow, Sian R. Nieduszynska, Carolin A. Müller, Conrad A. Nieduszynski:
OriDB, the DNA replication origin database updated and extended. 682-686 - Ke Jin, Jingjing Li, Frederick S. Vizeacoumar, Zhijian Li, Renqiang Min, Lee Zamparo, Franco J. Vizeacoumar, Alessandro Datti, Brenda J. Andrews, Charles Boone, Zhaolei Zhang:
PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae. 687-694 - Valerie Wood, Midori A. Harris, Mark D. McDowall,