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Nucleic 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 Duek Roggli
, 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 Wojciech 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 C. 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
, Egon 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 J. 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 Ariston de Carvalho 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,