Nucleic Acids Research, Volume 44

Volume 44, Number Database-Issue, January 2016

Nucleic acid sequence, structure, and regulation

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  Daniel J. Rigden, Xosé M. Fernández-Suárez, Michael Y. Galperin:
  The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. 1-6
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  Database resources of the National Center for Biotechnology Information. 7-19
• 
  Charles E. Cook, Mary Todd Bergman, Robert D. Finn, Guy Cochrane, Ewan Birney, Rolf Apweiler:
  The European Bioinformatics Institute in 2016: Data growth and integration. 20-26
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  The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. 27-37
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  Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak:
  Tools and data services registry: a community effort to document bioinformatics resources. 38-47
• 
  Guy Cochrane, Ilene Karsch-Mizrachi, Toshihisa Takagi:
  The International Nucleotide Sequence Database Collaboration. 48-50
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  Jun Mashima, Yuichi Kodama, Takehide Kosuge, Takatomo Fujisawa, Toshiaki Katayama, Hideki Nagasaki, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi:
  DNA data bank of Japan (DDBJ) progress report. 51-57
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  Richard Gibson, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Swapna Pallreddy, Nima Pakseresht, Jeena Rajan, Marc Rossello, Nicole Silvester, Dimitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane:
  Biocuration of functional annotation at the European nucleotide archive. 58-66
• 
  Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers:
  GenBank. 67-72
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  Paul A. Kitts, Deanna M. Church, Françoise Thibaud-Nissen, Jinna Choi, Vichet Hem, Victor Sapojnikov, Robert G. Smith, Tatiana A. Tatusova, Charlie Xiang, Andrey Zherikov, Michael DiCuccio, Terence D. Murphy, Kim D. Pruitt, Avi Kimchi:
  Assembly: a resource for assembled genomes at NCBI. 73-80
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  Robert Hubley, Robert D. Finn, Jody Clements, Sean R. Eddy, Thomas A. Jones, Weidong Bao, Arian F. A. Smit, Travis J. Wheeler:
  The Dfam database of repetitive DNA families. 81-89
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  Jörg Fallmann, Vitaly Sedlyarov, Andrea Tanzer, Pavel Kovarik, Ivo L. Hofacker:
  AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements. 90-95
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  Aline Dousse, Thomas Junier, Evgeny M. Zdobnov:
  CEGA - a catalog of conserved elements from genomic alignments. 96-100
• 
  Michal Chorev, Lotem Guy, Liran Carmel:
  JuncDB: an exon-exon junction database. 101-109
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  Anthony Mathelier, Oriol Fornes, David J. Arenillas, Chih-Yu Chen, Grégoire Denay, Jessica J. Y. Lee, Wenqiang Shi, Casper Shyr, Ge Tan, Rebecca Worsley-Hunt, Allen W. Zhang, François Parcy, Boris Lenhard, Albin Sandelin, Wyeth W. Wasserman:
  JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. 110-115
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  Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Anastasiia V. Soboleva, Artem S. Kasianov, Haitham Ashoor, Wail Ba-alawi, Vladimir B. Bajic, Yulia A. Medvedeva, Fedor A. Kolpakov, Vsevolod J. Makeev:
  HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. 116-125
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  Robert Lesurf, Kelsy C. Cotto, Grace Wang, Malachi Griffith, Katayoon Kasaian, Steven J. M. Jones, Stephen B. Montgomery, Obi L. Griffith:
  ORegAnno 3.0: a community-driven resource for curated regulatory annotation. 126-132
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  Socorro Gama-Castro, Heladia Salgado, Alberto Santos-Zavaleta, Daniela Ledezma-Tejeida, Luis Muñiz-Rascado, Jair Santiago García-Sotelo, Kevin Alquicira-Hernández, Irma Martínez-Flores, Lucia Pannier, Jaime Abraham Castro-Mondragón, Alejandra Medina-Rivera, Hilda Solano-Lira, César Bonavides-Martínez, Ernesto Pérez-Rueda, Shirley Alquicira-Hernández, Liliana Porrón-Sotelo, Alejandra López-Fuentes, Anastasia Hernández-Koutoucheva, Victor del Moral-Chávez, Fabio Rinaldi, Julio Collado-Vides:
  RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. 133-143
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  Olga Zanegina, Dmitry D. Kirsanov, Eugene Baulin, Anna S. Karyagina, Andrei Alexeevski, Sergei A. Spirin:
  An updated version of NPIDB includes new classifications of DNA-protein complexes and their families. 144-153
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  Fengbiao Mao, Luoyuan Xiao, Xianfeng Li, Jialong Liang, Huajing Teng, Wanshi Cai, Zhongsheng Sun:
  RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins. 154-163
• 
  Aziz Khan, Xuegong Zhang:
  dbSUPER: a database of super-enhancers in mouse and human genome. 164-171
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  Yanjun Wei, Shumei Zhang, Shipeng Shang, Bin Zhang, Song Li, Xinyu Wang, Fang Wang, Jianzhong Su, Qiong Wu, Hongbo Liu, Yan Zhang:
  SEA: a super-enhancer archive. 172-179
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  Maciej Szymanski, Andrzej Zielezinski, Jan Barciszewski, Volker A. Erdmann, Wojciech M. Karlowski:
  5SRNAdb: an information resource for 5S ribosomal RNAs. 180-183
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  Patricia P. Chan, Todd M. Lowe:
  GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. 184-189
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  Georgios K. Georgakilas, Ioannis S. Vlachos, Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ilias Kanellos, Panayiotis Tsanakas, Dimitris Dellis, Athanasios Fevgas, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
  DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. 190-195
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  Ling-Ling Zheng, Jun-Hao Li, Jie Wu, Wen-Ju Sun, Shun Liu, Ze-Lin Wang, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu:
  deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. 196-202
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  Yi Zhao, Hui Li, Shuangsang Fang, Yue Kang, Wei Wu, Yajing Hao, Ziyang Li, Dechao Bu, Ninghui Sun, Michael Q. Zhang, Runsheng Chen:
  NONCODE 2016: an informative and valuable data source of long non-coding RNAs. 203-208
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  Yu-Chen Liu, Jianrong Li, Chuan-Hu Sun, Erik Andrews, Rou-Fang Chao, Feng-Mao Lin, Shun-Long Weng, Sheng-Da Hsu, Chieh-Chen Huang, Chao Cheng, Chun-Chi Liu, Hsien-Da Huang:
  CircNet: a database of circular RNAs derived from transcriptome sequencing data. 209-215
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  Yuk Yee Leung, Pavel P. Kuksa, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, Li-San Wang:
  DASHR: database of small human noncoding RNAs. 216-222
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  David Rosenkranz:
  piRNA cluster database: a web resource for piRNA producing loci. 223-230
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  Maria D. Paraskevopoulou, Ioannis S. Vlachos, Dimitra Karagkouni, Georgios K. Georgakilas, Ilias Kanellos, Thanasis Vergoulis, Konstantinos Zagganas, Panayiotis Tsanakas, Evangelos Floros, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
  DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. 231-238
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  Chih-Hung Chou, Nai-Wen Chang, Sirjana Shrestha, Sheng-Da Hsu, Yu-Ling Lin, Wei-Hsiang Lee, Chi-Dung Yang, Hsiao-Chin Hong, Ting-Yen Wei, Siang-Jyun Tu, Tzi-Ren Tsai, Shu-Yi Ho, Ting-Yan Jian, Hsin-Yi Wu, Pin-Rong Chen, Nai-Chieh Lin, Hsin-Tzu Huang, Tzu-Ling Yang, Chung-Yuan Pai, Chun-San Tai, Wen-Liang Chen, Chia-Yen Huang, Chun-Chi Liu, Shun-Long Weng, Kuang-Wen Liao, Wen-Lian Hsu, Hsien-Da Huang:
  miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. 239-247
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  Jiang Wang, Tao Liu, Bo Zhao, Qixuan Lu, Zheng Wang, Yuan Cao, Wuju Li:
  sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria. 248-253
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  Shang-Qian Xie, Peng Nie, Yan Wang, Hongwei Wang, Hongyu Li, Zhilong Yang, Yizhi Liu, Jian Ren, Zhi Xie:
  RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling. 254-258
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  Wen-Ju Sun, Jun-Hao Li, Shun Liu, Jie Wu, Hui Zhou, Liang-Hu Qu, Jian-Hua Yang:
  RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data. 259-265
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  Sri Devan Appasamy, Hazrina Yusof Hamdani, Effirul Ikhwan Ramlan, Mohd Firdaus Raih:
  InterRNA: a database of base interactions in RNA structures. 266-271
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  Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codó, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Josep Ramón Goñi, Modesto Orozco, Josep Lluis Gelpí:
  BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. 272-278

Protein sequence and structure, motifs, and domains

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  Robert D. Finn, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Jaina Mistry, Alex L. Mitchell, Simon C. Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, Gustavo A. Salazar, John G. Tate, Alex Bateman:
  The Pfam protein families database: towards a more sustainable future. 279-285
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  Jaime Huerta-Cepas, Damian Szklarczyk, Kristoffer Forslund, Helen Cook, Davide Heller, Mathias C. Walter, Thomas Rattei, Daniel R. Mende, Shinichi Sunagawa, Michael Kuhn, Lars Juhl Jensen, Christian von Mering, Peer Bork:
  eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. 286-293
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  Holger Dinkel, Kim Van Roey, Sushama Michael, Manjeet Kumar, Bora Uyar, Brigitte Altenberg, Vladislava Milchevskaya, Melanie Schneider, Helen Kühn, Annika Behrendt, Sophie Luise Dahl, Victoria Damerell, Sandra Diebel, Sara Kalman, Steffen Klein, Arne C. Knudsen, Christina Mäder, Sabina Merrill, Angelina Staudt, Vera Thiel, Lukas Welti, Norman E. Davey, Francesca Diella, Toby J. Gibson:
  ELM 2016 - data update and new functionality of the eukaryotic linear motif resource. 294-300
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  Zejun Zheng, Alexander Goncearenco, Igor N. Berezovsky:
  Nucleotide binding database NBDB - a collection of sequence motifs with specific protein-ligand interactions. 301-307
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  Rhonald C. Lua, Stephen J. Wilson, Daniel M. Konecki, Angela D. Wilkins, Eric Venner, Daniel H. Morgan, Olivier Lichtarge:
  UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures. 308-312
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  Chunlei Wu, Xuefeng Jin, Ginger Tsueng, Cyrus Afrasiabi, Andrew I. Su:
  BioGPS: building your own mash-up of gene annotations and expression profiles. 313-316
• 
  Ian Sillitoe, Nicholas Furnham:
  FunTree: advances in a resource for exploring and contextualising protein function evolution. 317-323
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  Volodimir Olexiouk, Jeroen Crappé, Steven Verbruggen, Kenneth Verheggen, Lennart Martens, Gerben Menschaert:
  sORFs.org: a repository of small ORFs identified by ribosome profiling. 324-329
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  Yi-Chien Chang, Zhenjun Hu, John Rachlin, Brian P. Anton, Simon Kasif, Richard J. Roberts, Martin Steffen:
  COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. 330-335
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  Huaiyu Mi, Sagar Poudel, Anushya Muruganujan, John T. Casagrande, Paul D. Thomas:
  PANTHER version 10: expanded protein families and functions, and analysis tools. 336-342
• 
  Neil D. Rawlings, Alan J. Barrett, Robert D. Finn:
  Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors. 343-350
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  José G. Pérez-Silva, Yaiza Español, Gloria Velasco, Víctor Quesada:
  The Degradome database: expanding roles of mammalian proteases in life and disease. 351-355
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  Vignir Ísberg, Stefan Mordalski, Christian Munk, Krzysztof Rataj, Kasper Harpsøe, Alexander S. Hauser, Bas Vroling, Andrzej J. Bojarski, Gert Vriend, David E. Gloriam:
  GPCRdb: an information system for G protein-coupled receptors. 356-364
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  Albert J. Kooistra, Georgi K. Kanev, Oscar P. J. van Linden, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf:
  KLIFS: a structural kinase-ligand interaction database. 365-371
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  Milton H. Saier Jr., Vamsee S. Reddy, Brian V. Tsu, Muhammad Saad Ahmed, Chun Li, Gabriel Moreno-Hagelsieb:
  The Transporter Classification Database (TCDB): recent advances. 372-379
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  Damian Szklarczyk, Alberto Santos, Christian von Mering, Lars Juhl Jensen, Peer Bork, Michael Kuhn:
  STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. 380-384
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  Sameer Velankar, Glen van Ginkel, Younes Alhroub, Gary M. Battle, John M. Berrisford, Matthew J. Conroy, Jose M. Dana, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, Ingvar C. Lagerstedt, Saqib Mir, Manuel A. Fernandez Montecelo, Abhik Mukhopadhyay, Thomas J. Oldfield, Ardan Patwardhan, Eduardo Sanz-García, Sanchayita Sen, Robert A. Slowley, Michael E. Wainwright, Mandar S. Deshpande, Andrii Iudin, Gaurav Sahni, José Salavert Torres, Miriam Hirshberg, Lora Mak, Nurul Nadzirin, David R. Armstrong, Alice R. Clark, Oliver S. Smart, Paul K. Korir, Gerard J. Kleywegt:
  PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. 385-395
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  Catherine L. Lawson, Ardan Patwardhan, Matthew L. Baker, Corey Hryc, Eduardo Sanz-García, Brian P. Hudson, Ingvar C. Lagerstedt, Steven J. Ludtke, Grigore Pintilie, Raul Sala, John D. Westbrook, Helen M. Berman, Gerard J. Kleywegt, Wah Chiu:
  EMDataBank unified data resource for 3DEM. 396-403
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  Su Datt Lam, Natalie L. Dawson, Sayoni Das, Ian Sillitoe, Paul Ashford, David A. Lee, Sonja Lehtinen, Christine A. Orengo, Jonathan G. Lees:
  Gene3D: expanding the utility of domain assignments. 404-409
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  Arumugam Gandhimathi, Pritha Ghosh, Sridhar Hariharaputran, Oommen K. Mathew, Ramanathan Sowdhamini:
  PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. 410-414
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  Hongchun Li, Yuan-Yu Chang, Lee-Wei Yang, Ivet Bahar:
  iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. 415-422
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  Thomas Hrabe, Zhanwen Li, Mayya Sedova, Piotr Rotkiewicz, Lukasz Jaroszewski, Adam Godzik:
  PDBFlex: exploring flexibility in protein structures. 423-428
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  Rita Pancsa, Mihaly Varadi, Peter Tompa, Wim F. Vranken:
  Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. 429-434
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  Kai-Yao Huang, Min-Gang Su, Hui-Ju Kao, Yun-Chung Hsieh, Jhih-Hua Jhong, Kuang-Hao Cheng, Hsien-Da Huang, Tzong-Yi Lee:
  dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. 435-446
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  Juan Antonio Vizcaíno, Attila Csordas, Noemi del-Toro, José A. Dianes, Johannes Griss, Ilias Lavidas, Gerhard Mayer, Yasset Pérez-Riverol, Florian Reisinger, Tobias Ternent, Qing-Wei Xu, Rui Wang, Henning Hermjakob:
  2016 update of the PRIDE database and its related tools. 447-456

Metabolic and signalling pathways, enzymes

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  Minoru Kanehisa, Yoko Sato, Masayuki Kawashima, Miho Furumichi, Mao Tanabe:
  KEGG as a reference resource for gene and protein annotation. 457-462
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  Manish Sud, Eoin Fahy, Dawn Cotter, Kenan Azam, Ilango Vadivelu, Charles F. Burant, Arthur Edison, Oliver Fiehn, Richard M. Higashi, K. Sreekumaran Nair, Susan Sumner, Shankar Subramaniam:
  Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. 463-470
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  Ron Caspi, Richard Billington, Luciana Ferrer, Hartmut Foerster, Carol A. Fulcher, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne M. Paley, Pallavi Subhraveti, Daniel S. Weaver, Peter D. Karp:
  The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. 471-480
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  Antonio Fabregat, Konstantinos Sidiropoulos, Phani V. Garapati, Marc Gillespie, Kerstin Hausmann, Robin Haw, Bijay Jassal, Steven Jupe, Florian Korninger, Sheldon J. McKay, Lisa Matthews, Bruce May, Marija Milacic, Karen Rothfels, Veronica Shamovsky, Marissa Webber, Joel Weiser, Mark Williams, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
  The Reactome pathway Knowledgebase. 481-487
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  Martina Kutmon, Anders Riutta, Nuno Nunes, Kristina Hanspers, Egon L. Willighagen, Anwesha Bohler, Jonathan Mélius, Andra Waagmeester, Sravanthi R. Sinha, Ryan A. Miller, Susan L. Coort, Elisa Cirillo, Bart Smeets, Chris T. A. Evelo, Alexander R. Pico:
  WikiPathways: capturing the full diversity of pathway knowledge. 488-494
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  Tanvir Sajed, Ana Marcu, Miguel Ramirez-Gaona, Allison Pon, An Chi Guo, Craig Knox, Michael Wilson, Jason R. Grant, Yannick Djoumbou, David S. Wishart:
  ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. 495-501
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  Jörg Wicker, Tim Lorsbach, Martin Gütlein, Emanuel Schmid, Diogo Latino, Stefan Kramer, Kathrin Fenner:
  enviPath - The environmental contaminant biotransformation pathway resource. 502-508
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  Dennis Klementz, Kersten Döring, Xavier Lucas, Kiran K. Telukunta, Anika Erxleben, Denise Deubel, Astrid Erber, Irene Santillana, Oliver S. Thomas, Andreas Bechthold, Stefan Günther:
  StreptomeDB 2.0 - an extended resource of natural products produced by streptomycetes. 509-514
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  Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, Nathan E. Lewis:
  BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. 515-522
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  Sébastien Moretti, Olivier Martin, T. Van Du Tran, Alan J. Bridge, Anne Morgat, Marco Pagni:
  MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. 523-526
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  Qiancheng Shen, Guanqiao Wang, Shuai Li, Xinyi Liu, Shaoyong Lu, Zhongjie Chen, Kun Song, Junhao Yan, Lv Geng, Zhimin Huang, Wenkang Huang, Guoqiang Chen, Jian Zhang:
  ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks. 527-535
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  Max Kotlyar, Chiara Pastrello, Nicholas Sheahan, Igor Jurisica:
  Integrated interactions database: tissue-specific view of the human and model organism interactomes. 536-541
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  Céline M. Labbé, Mélaine A. Kuenemann, Barbara Zarzycka, Gert Vriend, Gerry A. F. Nicolaes, David Lagorce, Maria A. Miteva, Bruno O. Villoutreix, Olivier Sperandio:
  iPPI-DB: an online database of modulators of protein-protein interactions. 542-547
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  Livia Perfetto, Leonardo Briganti, Alberto Calderone, Andrea Cerquone Perpetuini, Marta Iannuccelli, Francesca Langone, Luana Licata, Milica Marinkovic, Anna Mattioni, Theodora Pavlidou, Daniele Peluso, Lucia Lisa Petrilli, Stefano Pirrò, Daniela Posca, Elena Santonico, Alessandra Silvestri, Filomena Spada, Luisa Castagnoli, Gianni Cesareni:
  SIGNOR: a database of causal relationships between biological entities. 548-554
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  Erich J. Baker, Jason A. Bubier, Timothy Reynolds, Michael A. Langston, Elissa J. Chesler:
  GeneWeaver: data driven alignment of cross-species genomics in biology and disease. 555-559
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  Yoav D. Shaul, Bingbing Yuan, Prathapan Thiru, Andy Nutter-Upham, Scott McCallum, Carolyn Lanzkron, George W. Bell, David M. Sabatini:
  MERAV: a tool for comparing gene expression across human tissues and cell types. 560-566
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  Radek Szklarczyk, Wout Megchelenbrink, Pavel Cizek, Marie Ledent, Gonny Velemans, Damian Szklarczyk, Martijn A. Huynen:
  WeGET: predicting new genes for molecular systems by weighted co-expression. 567-573

Viruses, bacteria, protozoa and fungi

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  Paul Julian Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Jay C. Humphrey, Arnaud Kerhornou, Julia Khobova, Naveen K. Aranganathan, Nicholas Langridge, Ernesto Lowy-Gallego, Mark D. McDowall, Uma Maheswari, Michael Nuhn, Chuang Kee Ong, Bert Overduin, Michael Paulini, Helder Pedro, Emily Perry, Giulietta Spudich, Electra Tapanari, Brandon Walts, Gareth Williams, Marcela K. Tello-Ruiz, Joshua C. Stein, Sharon Wei, Doreen Ware, Daniel M. Bolser, Kevin L. Howe, Eugene Kulesha, Daniel Lawson, Gareth Maslen, Daniel M. Staines:
  Ensembl Genomes 2016: more genomes, more complexity. 574-580
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  Carola Söhngen, Adam Podstawka, Boyke Bunk, Dorothea Gleim, Anna Vetcininova, Lorenz Christian Reimer, Christian Ebeling, Cezar Pendarovski, Jörg Overmann:
  BacDive - The Bacterial Diversity Metadatabase in 2016. 581-585
• 
  Daniel Greuter, Alexander Loy, Matthias Horn, Thomas Rattei:
  probeBase - an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016. 586-589
• 
  Andreas Wilke, Jared Bischof, Wolfgang Gerlach, Elizabeth M. Glass, Travis Harrison, Kevin P. Keegan, Tobias Paczian, William L. Trimble, Saurabh Bagchi, Ananth Grama, Somali Chaterji, Folker Meyer:
  The MG-RAST metagenomics database and portal in 2015. 590-594
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  Alex L. Mitchell, François Bucchini, Guy Cochrane, Hubert Denise, Petra ten Hoopen, Matthew Fraser, Sebastien Pesseat, Simon C. Potter, Maxim Scheremetjew, Peter Sterk, Robert D. Finn:
  EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data. 595-603
• 
  Samuel C. Forster, Hilary P. Browne, Nitin Kumar, Martin Hunt, Hubert Denise, Alex L. Mitchell, Robert D. Finn, Trevor D. Lawley:
  HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. 604-609
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  Hyeonsoo Jeong, Samsun Sung, Taehyung Kwon, Minseok Seo, Kelsey Caetano-Anollés, Sang Ho Choi, Seoae Cho, Arshan Nasir, Heebal Kim:
  HGTree: database of horizontally transferred genes determined by tree reconciliation. 610-619
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  Marco Moretto, Paolo Sonego, Nicolas Dierckxsens, Matteo Brilli, Luca Bianco, Daniela Ledezma-Tejeida, Socorro Gama-Castro, Marco Galardini, Chiara Romualdi, Kris Laukens, Julio Collado-Vides, Pieter Meysman, Kristof Engelen:
  COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. 620-623
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  Adil Salhi, Magbubah Essack, Aleksandar Radovanovic, Benoit Marchand, Salim Bougouffa, André Antunes, Marta Filipa Simões, Feras F. Lafi, Olaa A. Motwalli, Ameerah Bokhari, Tariq Malas, Soha Al Amoudi, Ghofran Othum, Intikhab Alam, Katsuhiko Mineta, Xin Gao, Robert Hoehndorf, John A. C. Archer, Takashi Gojobori, Vladimir B. Bajic:
  DESM: portal for microbial knowledge exploration systems. 624-633
• 
  Akanksha Rajput, Karambir Kaur, Manoj Kumar:
  SigMol: repertoire of quorum sensing signaling molecules in prokaryotes. 634-639
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  Keren Lasker, Jared M. Schrader, Yifei Men, Tyler Marshik, David L. Dill, Harley H. McAdams, Lucy Shapiro:
  CauloBrowser: A systems biology resource for Caulobacter crescentus. 640-645
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  Geoffrey L. Winsor, Emma J. Griffiths, Raymond Lo, Bhavjinder K. Dhillon, Julie A. Shay, Fiona S. L. Brinkman:
  Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. 646-653
• 
  Raphael H. Michna, Bingyao Zhu, Ulrike Mäder, Jörg Stülke:
  SubtiWiki 2.0 - an integrated database for the model organism Bacillus subtilis. 654-662
• 
  Michael A. Peabody, Matthew R. Laird, Caitlyn Vlasschaert, Raymond Lo, Fiona S. L. Brinkman:
  PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures. 663-668
• 
  Valerie Eichinger, Thomas Nussbaumer, Alexander Platzer, Marc-André Jehl, Roland Arnold, Thomas Rattei:
  EffectiveDB - updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. 669-674
• 
  Bharathi Reddy Kunduru, Sanjana Anilkumar Nair, Thenmalarchelvi Rathinavelan:
  EK3D: an E. coli K antigen 3-dimensional structure database. 675-681
• 
  Zhi Ruan, Ye Feng:
  BacWGSTdb, a database for genotyping and source tracking bacterial pathogens. 682-687
• 
  Helder Pedro, Uma Maheswari, Martin Urban, Alistair George Irvine, Alayne Cuzick, Mark D. McDowall, Daniel M. Staines, Eugene Kulesha, Kim Elizabeth Hammond-Kosack, Paul Julian Kersey:
  PhytoPath: an integrative resource for plant pathogen genomics. 688-693
• 
  Lihong Chen, Dandan Zheng, Bo Liu, Jian Yang, Qi Jin:
  VFDB 2016: hierarchical and refined dataset for big data analysis - 10 years on. 694-697
• 
  Travis K. Sheppard, Benjamin C. Hitz, Stacia R. Engel, Giltae Song, Rama Balakrishnan, Gail Binkley, Maria C. Costanzo, Kyla S. Dalusag, Janos Demeter, Sage T. Hellerstedt, Kalpana Karra, Robert S. Nash, Kelley M. Paskov, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, J. Michael Cherry:
  The Saccharomyces Genome Database Variant Viewer. 698-702
• 
  Jonathan Burns, Denys Kukushkin, Kelsi Lindblad, Xiao Chen, Natasa Jonoska, Laura F. Landweber:
  <mds_ies_db>: a database of ciliate genome rearrangements. 703-709

Human genome, model organisms, comparative genomics

• 
  Andrew D. Yates, Wasiu A. Akanni, M. Ridwan Amode, Daniel Barrell, Konstantinos Billis, Denise Carvalho-Silva, Carla A. Cummins, Peter Clapham, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Nathan Johnson, Thomas Juettemann, Stephen Keenan, Ilias Lavidas, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Michael Nuhn, Anne Parker, Mateus Patricio, Miguel Pignatelli, Matthew Rahtz, Harpreet Singh Riat, Daniel Sheppard, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Jennifer L. Harrow, Matthieu Muffato, Emily Perry, Magali Ruffier, Giulietta Spudich, Stephen J. Trevanion, Fiona Cunningham, Bronwen L. Aken, Daniel R. Zerbino, Paul Flicek:
  Ensembl 2016. 710-716
• 
  Matthew L. Speir, Ann S. Zweig, Kate R. Rosenbloom, Brian J. Raney, Benedict Paten, Parisa Nejad, Brian T. Lee, Katrina Learned, Donna Karolchik, Angie S. Hinrichs, Steven G. Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Pauline A. Fujita, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent:
  The UCSC Genome Browser database: 2016 update. 717-725
• 
  Cricket A. Sloan, Esther T. Chan, Jean M. Davidson, Venkat S. Malladi, J. Seth Strattan, Benjamin C. Hitz, Idan Gabdank, Aditi K. Narayanan, Marcus Ho, Brian T. Lee, Laurence D. Rowe, Timothy R. Dreszer, Greg Roe, Nikhil R. Podduturi, Forrest Tanaka, Eurie L. Hong, J. Michael Cherry:
  ENCODE data at the ENCODE portal. 726-732
• 
  Nuala A. O'Leary, Mathew W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Richard McVeigh, Bhanu Rajput, Barbara Robbertse, Brian Smith-White, Danso Ako-Adjei, Alexander Astashyn, Azat Badretdin, Yiming Bao, Olga Blinkova, Vyacheslav Brover, Vyacheslav Chetvernin, Jinna Choi, Eric Cox, Olga D. Ermolaeva, Catherine M. Farrell, Tamara Goldfarb, Tripti Gupta, Daniel H. Haft, Eneida Hatcher, Wratko Hlavina, Vinita S. Joardar, Vamsi K. Kodali, Wenjun Li, Donna R. Maglott, Patrick Masterson, Kelly M. McGarvey, Michael R. Murphy, Kathleen O'Neill, Shashikant Pujar, Sanjida H. Rangwala, Daniel Rausch, Lillian D. Riddick, Conrad L. Schoch, Andrei Shkeda, Susan S. Storz, Hanzhen Sun, Françoise Thibaud-Nissen, Igor Tolstoy, Raymond E. Tully, Anjana R. Vatsan, Craig Wallin, David Webb, Wendy Wu, Melissa J. Landrum, Avi Kimchi, Tatiana A. Tatusova, Michael DiCuccio, Paul A. Kitts, Terence D. Murphy, Kim D. Pruitt:
  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. 733-745
• 
  Robert Petryszak, Maria Keays, Y. Amy Tang, Nuno A. Fonseca, Elisabet Barrera, Tony Burdett, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Simon Jupp, Satu Koskinen, Oliver Mannion, Laura Huerta, Karine Megy, Catherine Snow, Eleanor Williams, Mitra Barzine, Emma Hastings, Hendrik Weisser, James C. Wright, Pankaj Jaiswal, Wolfgang Huber, Jyoti Choudhary, Helen E. Parkinson, Alvis Brazma:
  Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants. 746-752
• 
  Virginia Savova, Jon Patsenker, Sébastien Vigneau, Alexander A. Gimelbrant:
  NAR Breakthrough Article: dbMAE: the database of autosomal monoallelic expression. 753-756
• 
  Stefanie Seltmann, Fritz Lekschas, Robert Müller, Harald Stachelscheid, Marie-Sophie Bittner, Weiping Zhang, Luam Kidane, Anna Seriola, Anna Veiga, Glyn Stacey, Andreas Kurtz:
  hPSCreg - the human pluripotent stem cell registry. 757-763
• 
  Holger Brandl, HongKee Moon, Miquel Vila-Farré, Shang-Yun Liu, Ian Henry, Jochen C. Rink:
  PlanMine - a mineable resource of planarian biology and biodiversity. 764-773
• 
  Kevin L. Howe, Bruce J. Bolt, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Thomas A. Down, Sibyl Gao, Christian A. Grove, Todd W. Harris, Ranjana Kishore, Raymond Y. N. Lee, Jane Lomax, Yuling Li, Hans-Michael Müller, Cecilia Nakamura, Paulo A. S. Nuin, Michael Paulini, Daniela Raciti, Gary Schindelman, Eleanor Stanley, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Adam Wright, Karen Yook, Matthew Berriman, Paul J. Kersey, Tim Schedl, Lincoln Stein, Paul W. Sternberg:
  WormBase 2016: expanding to enable helminth genomic research. 774-780
• 
  Anthony Santella, Ismar Kovacevic, Laura A. Herndon, David H. Hall, Zhuo Du, Zhirong Bao:
  Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model. 781-785
• 
  Helen Attrill, Kathleen Falls, Joshua L. Goodman, Gillian H. Millburn, Giulia Antonazzo, Alix J. Rey, Steven J. Marygold:
  FlyBase: establishing a Gene Group resource for Drosophila melanogaster. 786-792
• 
  Christine G. Elsik, Aditi Tayal, Colin M. Diesh, Deepak R. Unni, Marianne L. Emery, Hung N. Nguyen, Darren E. Hagen:
  Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. 793-800
• 
  Chuanlin Yin, Gengyu Shen, Dianhao Guo, Shuping Wang, Xingzhou Ma, Huamei Xiao, Jinding Liu, Zan Zhang, Ying Liu, Yiqun Zhang, Kaixiang Yu, Shuiqing Huang, Fei Li:
  InsectBase: a resource for insect genomes and transcriptomes. 801-807
• 
  Matija Brozovic, Cyril Martin, Christelle Dantec, Delphine Dauga, Mickaël Mendez, Paul Simion, Madeline Percher, Baptiste Laporte, Céline Scornavacca, Anna Di Gregorio, Shigeki Fujiwara, Mathieu Gineste, Elijah K. Lowe, Jacques Piette, Claudia Racioppi, Filomena Ristoratore, Yasunori Sasakura, Naohito Takatori, C. Titus Brown, Frédéric Delsuc, Emmanuel J. P. Douzery, Carmela Gissi, Alex McDougall, Hiroki Nishida, Hitoshi Sawada, Billie J. Swalla, Hitoyoshi Yasuo, Patrick Lemaire:
  ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. 808-818
• 
  Juan Ignacio Alonso-Barba, Raza-Ur Rahman, Joachim Wittbrodt, Juan L. Mateo:
  MEPD: medaka expression pattern database, genes and more. 819-821
• 
  Gaurav K. Varshney, Suiyuan Zhang, Wuhong Pei, Ashrifia Adomako-Ankomah, Jacob Fohtung, Katherine Schaffer, Blake Carrington, Anoo Maskeri, Claire Slevin, Tyra G. Wolfsberg, Johan Ledin, Raman Sood, Shawn M. Burgess:
  CRISPRz: a database of zebrafish validated sgRNAs. 822-826
• 
  Zhi-Liang Hu, Carissa A. Park, James M. Reecy:
  Developmental progress and current status of the Animal QTLdb. 827-833
• 
  Christine G. Elsik, Deepak R. Unni, Colin M. Diesh, Aditi Tayal, Marianne L. Emery, Hung N. Nguyen, Darren E. Hagen:
  Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. 834-839
• 
  Carol J. Bult, Janan T. Eppig, Judith A. Blake, James A. Kadin, Joel E. Richardson:
  Mouse genome database 2016. 840-847
• 
  Eiru Kim, Sohyun Hwang, Hyojin Kim, Hongseok Shim, Byunghee Kang, Sunmo Yang, Jae Ho Shim, Seung Yeon Shin, Edward M. Marcotte, Insuk Lee:
  MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. 848-854
• 
  Robert L. Wilson, Christina McGuire, Timothy Mohun:
  Deciphering the mechanisms of developmental disorders: phenotype analysis of embryos from mutant mouse lines. 855-861

Genomic variation, diseases, and drugs

• 
  Melissa J. Landrum, Jennifer M. Lee, Mark Benson, Garth R. Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Jeffrey Hoover, Wonhee Jang, Kenneth S. Katz, Michael Ovetsky, George R. Riley, Amanjeev Sethi, Ray E. Tully, Ricardo Villamarín-Salomón, Wendy S. Rubinstein, Donna R. Maglott:
  ClinVar: public archive of interpretations of clinically relevant variants. 862-868
• 
  Mulin Jun Li, Zipeng Liu, Panwen Wang, Maria P. Wong, Matthew R. Nelson, Jean-Pierre A. Kocher, Meredith Yeager, Pak Chung Sham, Stephen J. Chanock, Zhengyuan Xia, Junwen Wang:
  GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. 869-876
• 
  Lucas D. Ward, Manolis Kellis:
  HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. 877-881
• 
  Dinanath Sulakhe, Bingqing Xie, Andrew Taylor, Mark D'Souza, Sandhya Balasubramanian, Somaye Hashemifar, Steven White, Utpal J. Dave, Gady Agam, Jinbo Xu, Sheng Wang, T. Conrad Gilliam, Natalia Maltsev:
  Lynx: a knowledge base and an analytical workbench for integrative medicine. 882-887
• 
  Liyuan Guo, Yang Du, Susu Qu, Jing Wang:
  rVarBase: an updated database for regulatory features of human variants. 888-893
• 
  Alexey Moskalev, Svetlana Zhikrivetskaya, Mikhail Shaposhnikov, Evgenia Dobrovolskaya, Roman Gurinovich, Oleg Kuryan, Aleksandr Pashuk, Leslie C. Jellen, Alex Aliper, Alex Peregudov, Alex Zhavoronkov:
  Aging Chart: a community resource for rapid exploratory pathway analysis of age-related processes. 894-899
• 
  Andrea M. Gazzo, Dorien Daneels, Elisa Cilia, Maryse Bonduelle, Marc Abramowicz, Sonia Van Dooren, Guillaume Smits, Tom Lenaerts:
  NAR Breakthrough Article: DIDA: A curated and annotated digenic diseases database. 900-907
• 
  Mara Kim, Brian A. Cooper, Rohit Venkat, Julie B. Phillips, Haley R. Eidem, Jibril Hirbo, Sashank Nutakki, Scott M. Williams, Louis J. Muglia, J. Anthony Capra, Kenneth Petren, Patrick Abbot, Antonis Rokas, Kriston L. McGary:
  GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. 908-916
• 
  Frederik Otzen Bagger, Damir Sasivarevic, Sina Hadi Sohi, Linea Gøricke Laursen, Sachin Pundhir, Casper Kaae Sønderby, Ole Winther, Nicolas Rapin, Bo T. Porse:
  BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis. 917-924
• 
  Jens Lichtenberg, Elisabeth F. Heuston, Tejaswini Mishra, Cheryl A. Keller, Ross C. Hardison, David M. Bodine:
  SBR-Blood: systems biology repository for hematopoietic cells. 925-931
• 
  Björn-Oliver Gohlke, Janette Nickel, Raik Otto, Mathias Dunkel, Robert Preissner:
  CancerResource - updated database of cancer-relevant proteins, mutations and interacting drugs. 932-937
• 
  Joseph E. Tym, Costas Mitsopoulos, Elizabeth A. Coker, Parisa Razaz, Amanda C. Schierz, Albert A. Antolin, Bissan Al-Lazikani:
  canSAR: an updated cancer research and drug discovery knowledgebase. 938-943
• 
  Jianrong Li, Chuan-Hu Sun, Wenyuan Li, Rou-Fang Chao, Chieh-Chen Huang, Xianghong Jasmine Zhou, Chun-Chi Liu:
  Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. 944-951
• 
  Pankaj Narang, Parashar Dhapola, Shantanu Chowdhury:
  BreCAN-DB: a repository cum browser of personalized DNA breakpoint profiles of cancer genomes. 952-958
• 
  Pora Kim, Feixiong Cheng, Junfei Zhao, Zhongming Zhao:
  ccmGDB: a database for cancer cell metabolism genes. 959-968
• 
  David Chisanga, Shivakumar Keerthikumar, Mohashin Pathan, Dinuka Ariyaratne, Hina Kalra, Stephanie Boukouris, Nidhi Abraham Mathew, Haidar Al Saffar, Lahiru Gangoda, Ching-Seng Ang, Oliver M. Sieber, John M. Mariadason, Ramanuj Dasgupta, Naveen K. Chilamkurti, Suresh Mathivanan:
  Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues. 969-974
• 
  I-Fang Chung, Chen-Yang Chen, Shih-Chieh Su, Chia-Yang Li, Kou-Juey Wu, Hsei-Wei Wang, Wei-Chung Cheng:
  DriverDBv2: a database for human cancer driver gene research. 975-979
• 
  Shangwei Ning, Jizhou Zhang, Peng Wang, Hui Zhi, Jianjian Wang, Yue Liu, Yue Gao, Maoni Guo, Ming Yue, Lihua Wang, Xia Li:
  Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers. 980-985
• 
  Nicholas Paul Gauthier, Ed Reznik, Jianjiong Gao, Selçuk Onur Sümer, Nikolaus Schultz, Chris Sander, Martin L. Miller:
  MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. 986-991
• 
  Omer An, Giovanni Marco Dall'Olio, Thanos P. Mourikis, Francesca D. Ciccarelli:
  NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. 992-999
• 
  Sung-Joon Park, Yusuke Komiyama, Hirofumi Suemori, Akihiro Umezawa, Kenta Nakai:
  OpenTein: a database of digital whole-slide images of stem cell-derived teratomas. 1000-1004
• 
  Anindya Bhattacharya, Yan Cui:
  SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions. 1005-1010
• 
  Jing Guo, Hui Liu, Jie Zheng:
  SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. 1011-1017
• 
  Michael C. Ryan, Wing Chung Wong, Robert Brown, Rehan Akbani, Xiaoping Su, Bradley M. Broom, James M. Melott, John N. Weinstein:
  TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. 1018-1022
• 
  Min Zhao, Pora Kim, Ramkrishna Mitra, Junfei Zhao, Zhongming Zhao:
  TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. 1023-1031
• 
  Shaini Joseph, Ram Shankar Barai, Rasika Bhujbalrao, Susan Idicula-Thomas:
  PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome. 1032-1035
• 
  Alex H. Wagner, Adam C. Coffman, Benjamin J. Ainscough, Nicholas C. Spies, Zachary L. Skidmore, Katie M. Campbell, Kilannin Krysiak, Deng Pan, Joshua F. McMichael, James M. Eldred, Jason R. Walker, Richard K. Wilson, Elaine R. Mardis, Malachi Griffith, Obi L. Griffith:
  DGIdb 2.0: mining clinically relevant drug-gene interactions. 1036-1044
• 
  Michael K. Gilson, Tiqing Liu, Michael Baitaluk, George Nicola, Linda Hwang, Jenny Chong:
  BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. 1045-1053
• 
  Christopher Southan, Joanna L. Sharman, Helen E. Benson, Elena Faccenda, Adam J. Pawson, Stephen P. H. Alexander, Oscar Peter Buneman, Anthony P. Davenport, John C. McGrath, John A. Peters, Michael Spedding, William A. Catterall, Doriano Fabbro, Jamie A. Davies, NC-IUPHAR:
  The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. 1054-1068
• 
  Hong Yang, Chu Qin, Ying Hong Li, Lin Tao, Jin Zhou, Chun Yan Yu, Feng Xu, Zhe Chen, Feng Zhu, Yuzong Chen:
  Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. 1069-1074
• 
  Michael Kuhn, Ivica Letunic, Lars Juhl Jensen, Peer Bork:
  The SIDER database of drugs and side effects. 1075-1079
• 
  Vishal B. Siramshetty, Janette Nickel, Christian Omieczynski, Björn-Oliver Gohlke, Malgorzata N. Drwal, Robert Preissner:
  WITHDRAWN - a resource for withdrawn and discontinued drugs. 1080-1086
• 
  Guangshun Wang, Xia Li, Zhe Wang:
  APD3: the antimicrobial peptide database as a tool for research and education. 1087-1093
• 
  Faiza Hanif Waghu, Ram Shankar Barai, Pratima Gurung, Susan Idicula-Thomas:
  CAMP_R3: a database on sequences, structures and signatures of antimicrobial peptides. 1094-1097
• 
  Piyush Agrawal, Sherry Bhalla, Salman Sadullah Usmani, Sandeep Singh, Kumardeep Chaudhary, Gajendra P. S. Raghava, Ankur Gautam:
  CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides. 1098-1103
• 
  Malak Pirtskhalava, Andrei E. Gabrielian, Phillip Cruz, Hannah L. Griggs, R. Burke Squires, Darrell E. Hurt, Maia Grigolava, Mindia Chubinidze, George Gogoladze, Boris Vishnepolsky, Vsevolod Alekseev, Alex Rosenthal, Michael Tartakovsky:
  DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides. 1104-1112
• 
  Areski Flissi, Yoann Dufresne, Juraj Michalik, Laurie Tonon, Stéphane Janot, Laurent Noé, Philippe Jacques, Valérie Leclère, Maude Pupin:
  Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing. 1113-1118
• 
  Sandeep Singh, Kumardeep Chaudhary, Sandeep Kumar Dhanda, Sherry Bhalla, Salman Sadullah Usmani, Ankur Gautam, Abhishek Tuknait, Piyush Agrawal, Deepika Mathur, Gajendra P. S. Raghava:
  SATPdb: a database of structurally annotated therapeutic peptides. 1119-1126
• 
  Bifang He, Guoshi Chai, Yaocong Duan, Zhiqiang Yan, Liuyang Qiu, Huixiong Zhang, Zechun Liu, Qiang He, Ke Han, Beibei Ru, Feng-Biao Guo, Hui Ding, Hao Lin, Xianlong Wang, Nini Rao, Peng Zhou, Jian Huang:
  BDB: biopanning data bank. 1127-1132

Plant databases

• 
  Marcela K. Tello-Ruiz, Joshua C. Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule, Justin Elser, Bo Wang, James Thomason, Daniel M. Bolser, Arnaud Kerhornou, Brandon Walts, Nuno A. Fonseca, Laura Huerta, Maria Keays, Y. Amy Tang, Helen E. Parkinson, Antonio Fabregat, Sheldon J. McKay, Joel Weiser, Peter D'Eustachio, Lincoln Stein, Robert Petryszak, Paul J. Kersey, Pankaj Jaiswal, Doreen Ware:
  Gramene 2016: comparative plant genomics and pathway resources. 1133-1140
• 
  Manuel Spannagl, Thomas Nussbaumer, Kai Christian Bader, Mihaela M. Martis, Michael Seidel, Karl G. Kugler, Heidrun Gundlach, Klaus F. X. Mayer:
  PGSB PlantsDB: updates to the database framework for comparative plant genome research. 1141-1147
• 
  Tao Zhang, Alexandre P. Marand, Jiming Jiang:
  PlantDHS: a database for DNase I hypersensitive sites in plants. 1148-1153
• 
  Chi-Nga Chow, Han-Qin Zheng, Nai-Yun Wu, Chia-Hung Chien, Hsien-Da Huang, Tzong-Yi Lee, Yi-Fan Chiang-Hsieh, Ping-Fu Hou, Tien-Yi Yang, Wen-Chi Chang:
  PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. 1154-1160
• 
  Andreu Paytuví Gallart, Antonio Hermoso Pulido, Irantzu Anzar Martínez de Lagrán, Walter Sanseverino, Riccardo Aiese Cigliano:
  GREENC: a Wiki-based database of plant lncRNAs. 1161-1166
• 
  Frédéric Bouché, Guillaume Lobet, Pierre Tocquin, Claire Périlleux:
  FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. 1167-1171
• 
  Information Commons for Rice (IC4R). 1172-1180
• 
  Sudhansu Dash, Jacqueline D. Campbell, Ethalinda K. S. Cannon, Alan M. Cleary, Wei Huang, Scott R. Kalberer, Vijay Karingula, Alex G. Rice, Jugpreet Singh, Pooja E. Umale, Nathan T. Weeks, Andrew P. Wilkey, Andrew D. Farmer, Steven B. Cannon:
  Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. 1181-1188
• 
  Jun Li, Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao:
  LegumeIP 2.0 - a platform for the study of gene function and genome evolution in legumes. 1189-1194
• 
  Carson M. Andorf, Ethalinda K. S. Cannon, John L. Portwood II, Jack M. Gardiner, Lisa C. Harper, Mary L. Schaeffer, Bremen L. Braun, Darwin A. Campbell, Abhinav G. Vinnakota, Venktanaga V. Sribalusu, Miranda Huerta, Kyoung Tak Cho, Kokulapalan Wimalanathan, Jacqueline D. Richter, Emily D. Mauch, Bhavani S. Rao, Scott M. Birkett, Taner Z. Sen, Carolyn J. Lawrence-Dill:
  MaizeGDB update: new tools, data and interface for the maize model organism database. 1195-1201

Other databases

• 
  Sunghwan Kim, Paul A. Thiessen, Evan Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han, Jane He, Siqian He, Benjamin A. Shoemaker, Jiyao Wang, Bo Yu, Jian Zhang, Stephen H. Bryant:
  PubChem Substance and Compound databases. 1202-1213
• 
  Janna Hastings, Gareth I. Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck:
  ChEBI in 2016: Improved services and an expanding collection of metabolites. 1214-1219
• 
  George Papadatos, Mark Davies, Nathan Dedman, Jon Chambers, Anna Gaulton, James Siddle, Richard Koks, Sean A. Irvine, Joe Pettersson, Nicholas T. Goncharoff, Anne Hersey, John P. Overington:
  SureChEMBL: a large-scale, chemically annotated patent document database. 1220-1228
• 
  Philip V. Toukach, Ksenia S. Egorova:
  Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts. 1229-1236
• 
  Kiyoko F. Aoki-Kinoshita, Sanjay Agravat, Nobuyuki P. Aoki, Sena Arpinar, Richard D. Cummings, Akihiro Fujita, Noriaki Fujita, Gerald M. Hart, Stuart M. Haslam, Toshisuke Kawasaki, Masaaki Matsubara, Kelley W. Moreman, Shujiro Okuda, Michael Pierce, René Ranzinger, Toshihide Shikanai, Daisuke Shinmachi, Elena Solovieva, Yoshinori Suzuki, Shinichiro Tsuchiya, Issaku Yamada, William S. York, Joseph Zaia, Hisashi Narimatsu:
  GlyTouCan 1.0 - The international glycan structure repository. 1237-1242
• 
  Julien Mariethoz, Khaled Khatib, Davide Alocci, Matthew P. Campbell, Niclas G. Karlsson, Nicolle H. Packer, Elaine H. Mullen, Frédérique Lisacek:
  SugarBindDB, a resource of glycan-mediated host-pathogen interactions. 1243-1250
• 
  Sarah E. Calvo, Karl R. Clauser, Vamsi K. Mootha:
  MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. 1251-1257
• 
  Anthony C. Smith, Alan J. Robinson:
  MitoMiner v3.1, an update on the mitochondrial proteomics database. 1258-1261
• 
  Dmitri Toren, Thomer Barzilay, Robi Tacutu, Gilad Lehmann, Khachik K. Muradian, Vadim E. Fraifeld:
  MitoAge: a database for comparative analysis of mitochondrial DNA, with a special focus on animal longevity. 1262-1265

Volume 44, Number Webserver-Issue, August 2016

Editorial

• 
  Gary Benson:
  Editorial: Nucleic Acids Research annual Web Server Issue in 2016. W1-W2

Articles

• 
  Enis Afgan, Dannon Baker, Marius van den Beek, Daniel J. Blankenberg, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Gregory Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, Jeremy Goecks:
  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. W3-W10
• 
  Peter Jehl, Jean Manguy, Denis C. Shields, Desmond G. Higgins, Norman E. Davey:
  ProViz - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. W11-W15
• 
  David Arndt, Jason R. Grant, Ana Marcu, Tanvir Sajed, Allison Pon, Yongjie Liang, David S. Wishart:
  PHASTER: a better, faster version of the PHAST phage search tool. W16-W21
• 
  Jochen Blom, Julian Kreis, Sebastian Spänig, Tobias Juhre, Claire Bertelli, Corinna Ernst, Alexander Goesmann:
  EDGAR 2.0: an enhanced software platform for comparative gene content analyses. W22-W28
• 
  Sascha Steinbiss, Fatima Silva-Franco, Brian P. Brunk, Bernardo Foth, Christiane Hertz-Fowler, Matthew Berriman, Thomas D. Otto:
  Companion: a web server for annotation and analysis of parasite genomes. W29-W34
• 
  Jongin Lee, Woonyoung Hong, Minah Cho, Mikang Sim, Daehwan Lee, Younhee Ko, Jaebum Kim:
  Synteny Portal: a web-based application portal for synteny block analysis. W35-W40
• 
  Daniel Veltri, Martha Malapi Wight, Jo Anne Crouch:
  SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species. W41-W45
• 
  Ofir Cohen, Shany Doron, Omri Wurtzel, Daniel Dar, Sarit Edelheit, Iris Karunker, Eran Mick, Rotem Sorek:
  Comparative transcriptomics across the prokaryotic tree of life. W46-W53
• 
  Todd M. Lowe, Patricia P. Chan:
  tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. W54-W57
• 
  Hansi Weißensteiner, Dominic Pacher, Anita Kloss-Brandstätter, Lukas Forer, Günther Specht, Hans-Jürgen Bandelt, Florian Kronenberg, Antonio Salas, Sebastian Schönherr:
  HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. W58-W63
• 
  Hansi Weißensteiner, Lukas Forer, Christian Fuchsberger, Bernd Schöpf, Anita Kloss-Brandstätter, Günther Specht, Florian Kronenberg, Sebastian Schönherr:
  mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud. W64-W69
• 
  Fahad Khalid, José Aguilar-Rodríguez, Andreas Wagner, Joshua L. Payne:
  Genonets server - a web server for the construction, analysis and visualization of genotype networks. W70-W76
• 
  Costas Bouyioukos, François Bucchini, Mohamed Elati, François Képès:
  GREAT: a web portal for Genome Regulatory Architecture Tools. W77-W82
• 
  Jüri Reimand, Tambet Arak, Priit Adler, Liis Kolberg, Sulev Reisberg, Hedi Peterson, Jaak Vilo:
  g: Profiler - a web server for functional interpretation of gene lists (2016 update). W83-W89
• 
  Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma'ayan:
  Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. W90-W97
• 
  Markus List, Nicolas Alcaraz, Martin Dissing-Hansen, Henrik J. Ditzel, Jan Mollenhauer, Jan Baumbach:
  KeyPathwayMinerWeb: online multi-omics network enrichment. W98-W104
• 
  Christoph Ogris, Thomas Helleday, Erik L. L. Sonnhammer:
  PathwAX: a web server for network crosstalk based pathway annotation. W105-W109
• 
  Christina Backes, Qurratulain T. Khaleeq, Eckart Meese, Andreas Keller:
  miEAA: microRNA enrichment analysis and annotation. W110-W116
• 
  Léon-Charles Tranchevent, Amin Ardeshirdavani, Sarah ElShal, Daniel Alcaide, Jan Aerts, Didier Auboeuf, Yves Moreau:
  Candidate gene prioritization with Endeavour. W117-W121
• 
  Yongqing Zhang, Xiaoyi Cao, Sheng Zhong:
  GeNemo: a search engine for web-based functional genomic data. W122-W127
• 
  Ioannis S. Vlachos, Thanasis Vergoulis, Maria D. Paraskevopoulou, Filopoimin Lykokanellos, Georgios K. Georgakilas, Penny Georgiou, Serafeim Chatzopoulos, Dimitra Karagkouni, Foteini Christodoulou, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
  DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. W128-W134
• 
  Yannan Fan, Keith Siklenka, Simran K. Arora, Paula Ribeiro, Sarah Kimmins, Jianguo Xia:
  miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis. W135-W141
• 
  Sergio Pulido-Tamayo, Jorge Duitama, Kathleen Marchal:
  EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis. W142-W146
• 
  Sasha Babicki, David Arndt, Ana Marcu, Yongjie Liang, Jason R. Grant, Adam Maciejewski, David S. Wishart:
  Heatmapper: web-enabled heat mapping for all. W147-W153
• 
  Song He, Haochen He, Wenjian Xu, Xin Huang, Shuai Jiang, Fei Li, Fuchu He, Xiaochen Bo:
  ICM: a web server for integrated clustering of multi-dimensional biomedical data. W154-W159
• 
  Fidel Ramírez, Devon Patrick Ryan, Björn A. Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, Thomas Manke:
  deepTools2: a next generation web server for deep-sequencing data analysis. W160-W165
• 
  Yuanwei Zhang, Qiguang Zang, Huan Zhang, Rongjun Ban, Yifan Yang, Furhan Iqbal, Ao Li, Qinghua Shi:
  DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data. W166-W175
• 
  Pedro Furió-Tarí, Sonia Tarazona, Toni Gabaldón, Anton J. Enright, Ana Conesa:
  spongeScan: A web for detecting microRNA binding elements in lncRNA sequences. W176-W180
• 
  Christophe Tav, Sébastien Tempel, Laurent Poligny, Fariza Tahi:
  miRNAFold: a web server for fast miRNA precursor prediction in genomes. W181-W184
• 
  Ling-Ling Zheng, Wei-Lin Xu, Shun Liu, Wen-Ju Sun, Jun-Hao Li, Jie Wu, Jian-Hua Yang, Liang-Hu Qu:
  tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. W185-W193
• 
  Alexey A. Sergushichev, Alexander A. Loboda, Abhishek Kumar Jha, Emma E. Vincent, Edward M. Driggers, Russell G. Jones, Edward J. Pearce, Maxim N. Artyomov:
  GAM: a web-service for integrated transcriptional and metabolic network analysis. W194-W200
• 
  Javier López-Ibáñez, Florencio Pazos, Monica Chagoyen:
  MBROLE 2.0 - functional enrichment of chemical compounds. W201-W204
• 
  Kansuporn Sriyudthsak, Ramon Francisco Pacquiao Mejia, Masanori Arita, Masami Y. Hirai:
  PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems. W205-W211
• 
  Francisco Salavert, Marta R. Hidalgo, Alicia Amadoz, Cankut Çubuk, Ignacio Medina, Daniel Crespo, José Carbonell-Caballero, Joaquín Dopazo:
  Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models. W212-W216
• 
  Hiroyuki Kuwahara, Meshari Alazmi, Xuefeng Cui, Xin Gao:
  MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. W217-W225
• 
  Baudoin Delépine, Vincent Libis, Pablo Carbonell, Jean-Loup Faulon:
  SensiPath: computer-aided design of sensing-enabling metabolic pathways. W226-W231
• 
  Jana Trifinopoulos, Lam-Tung Nguyen, Arndt von Haeseler, Bui Quang Minh:
  W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. W232-W235
• 
  Zilong He, Huangkai Zhang, Shenghan Gao, Martin J. Lercher, Wei-Hua Chen, Songnian Hu:
  Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees. W236-W241
• 
  Ivica Letunic, Peer Bork:
  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. W242-W245
• 
  Bruno Ribeiro-Gonçalves, Alexandre P. Francisco, Cátia Vaz, Mário Ramirez, João André Carriço:
  PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees. W246-W251
• 
  Jian Yang, Jixiang Liu, Liang Ouyang, Yi Chen, Bo Liu, Haoyang Cai:
  CTLPScanner: a web server for chromothripsis-like pattern detection. W252-W258
• 
  Hyerin Kim, NaNa Kang, Kyuhyeon An, Jae Hyung Koo, Min-Soo Kim:
  MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments. W259-W266
• 
  Juan C. Oliveros, Mònica Franch, Daniel Tabas-Madrid, David San-León, Lluis Montoliu, Pilar Cubas, Florencio Pazos:
  Breaking-Cas - interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes. W267-W271
• 
  Kornel Labun, Tessa G. Montague, James A. Gagnon, Summer B. Thyme, Eivind Valen:
  CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. W272-W276
• 
  Parashar Dhapola, Shantanu Chowdhury:
  QuadBase2: web server for multiplexed guanine quadruplex mining and visualization. W277-W283
• 
  Jirí Cerný, Paulína Bozíková, Bohdan Schneider:
  DNATCO: assignment of DNA conformers at dnatco.org. W284-W287
• 
  Przemyslaw Szalaj, Paul J. Michalski, Przemyslaw Wróblewski, Zhonghui Tang, Michal Kadlof, Giovanni Mazzocco, Yijun Ruan, Dariusz Plewczynski:
  3D-GNOME: an integrated web service for structural modeling of the 3D genome. W288-W293
• 
  Yang Wu, Rihao Qu, Yiming Huang, Binbin Shi, Mengrong Liu, Yang Li, Zhi John Lu:
  RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data. W294-W301
• 
  Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai:
  Rtools: a web server for various secondary structural analyses on single RNA sequences. W302-W307
• 
  Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash:
  incaRNAfbinv: a web server for the fragment-based design of RNA sequences. W308-W314
• 
  Marcin Magnus, Michal J. Boniecki, Wayne Dawson, Janusz M. Bujnicki:
  SimRNAweb: a web server for RNA 3D structure modeling with optional restraints. W315-W319
• 
  James Roll, Craig L. Zirbel, Blake A. Sweeney, Anton I. Petrov, Neocles Leontis:
  JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs. W320-W327
• 
  Chung-Han Yang, Cheng-Ting Shih, Kun-Tze Chen, Po-Han Lee, Ping-Han Tsai, Jian-Cheng Lin, Ching-Yu Yen, Tiao-Yin Lin, Chin Lung Lu:
  iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2. W328-W332
• 
  Juw Won Park, Sungbo Jung, Eric C. Rouchka, Yu-Ting Tseng, Yi Xing:
  rMAPS: RNA map analysis and plotting server for alternative exon regulation. W333-W338
• 
  Evan W. Floden, Paolo Di Tommaso, Maria Chatzou, Cedrik Magis, Cédric Notredame, Jia-Ming Chang:
  PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. W339-W343
• 
  Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal:
  ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. W344-W350
• 
  Liisa Holm, Laura M. Laakso:
  Dali server update. W351-W355
• 
  R. Gonzalo Parra, Nicholas P. Schafer, Leandro G. Radusky, Min-Yeh Tsai, A. Brenda Guzovsky, Peter G. Wolynes, Diego U. Ferreiro:
  Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics. W356-W360
• 
  Sheng Wang, Wei Li, Renyu Zhang, Shiwang Liu, Jinbo Xu:
  CoinFold: a web server for protein contact prediction and contact-assisted protein folding. W361-W366
• 
  Damiano Piovesan, Giovanni Minervini, Silvio C. E. Tosatto:
  The RING 2.0 web server for high quality residue interaction networks. W367-W374
• 
  Broto Chakrabarty, Nita Parekh:
  NAPS: Network Analysis of Protein Structures. W375-W382
• 
  Pawel Dabrowski-Tumanski, Wanda Niemyska, Pawel Pasznik, Joanna I. Sulkowska:
  LassoProt: server to analyze biopolymers with lassos. W383-W389
• 
  Jochen Ismer, Alexander S. Rose, Johanna K. S. Tiemann, Andrean Goede, Robert Preissner, Peter W. Hildebrand:
  SL2: an interactive webtool for modeling of missing segments in proteins. W390-W394
• 
  José Ramón López-Blanco, Alejandro Jesús Canosa-Valls, Yaohang Li, Pablo Chacón:
  RCD+: Fast loop modeling server. W395-W400
• 
  Thomas Gaillard, Roland H. Stote, Annick Dejaegere:
  PSSweb: protein structural statistics web server. W401-W405
• 
  Debswapna Bhattacharya, Jackson Nowotny, Renzhi Cao, Jianlin Cheng:
  3Drefine: an interactive web server for efficient protein structure refinement. W406-W409
• 
  Vikram Alva, Seung-Zin Nam, Johannes Söding, Andrei N. Lupas:
  The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. W410-W415
• 
  Joonghyun Ryu, Mokwon Lee, Jehyun Cha, Roman A. Laskowski, Seong Eon Ryu, Deok-Soo Kim:
  BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization. W416-W423
• 
  Dina Schneidman-Duhovny, Michal Hammel, John A. Tainer, Andrej Sali:
  FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. W424-W429
• 
  Sheng Wang, Wei Li, Shiwang Liu, Jinbo Xu:
  RaptorX-Property: a web server for protein structure property prediction. W430-W435
• 
  Hongjian Li, Kwong-Sak Leung, Man Hon Wong, Pedro J. Ballester:
  USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques. W436-W441
• 
  Jocelyn Sunseri, David Ryan Koes:
  Pharmit: interactive exploration of chemical space. W442-W448
• 
  Alexis Lamiable, Pierre Thévenet, Julien Rey, Marek Vavrusa, Philippe Derreumaux, Pierre Tufféry:
  PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex. W449-W454
• 
  Mauricio Esguerra, Alexey Siretskiy, Xabier Bello, Jessica Sallander, Hugo Gutiérrez-de-Terán:
  GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors. W455-W462
• 
  Alexander Greß, Vasily Ramensky, Joachim Büch, Andreas Keller, Olga V. Kalinina:
  StructMAn: annotation of single-nucleotide polymorphisms in the structural context. W463-W468
• 
  Douglas E. V. Pires, David B. Ascher:
  mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures. W469-W473
• 
  James Dunbar, Konrad Krawczyk, Jinwoo Leem, Claire Marks, Jaroslaw Nowak, Cristian Regep, Guy Georges, Sebastian Kelm, Bojana Popovic, Charlotte M. Deane:
  SAbPred: a structure-based antibody prediction server. W474-W478
• 
  Jaroslav Bendl, Jan Stourac, Eva Sebestova, Ondrej Vavra, Milos Musil, Jan Brezovsky, Jirí Damborský:
  HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. W479-W487
• 
  Nawar Malhis, Matthew Jacobson, Jörg Gsponer:
  MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences. W488-W493
• 
  Minghui Li, Franco L. Simonetti, Alexander Goncearenco, Anna R. Panchenko:
  MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions. W494-W501
• 
  Gyu Rie Lee, Chaok Seok:
  Galaxy7TM: flexible GPCR-ligand docking by structure refinement. W502-W506
• 
  Kun-Yi Hsin, Yukiko Matsuoka, Yoshiyuki Asai, Kyota Kamiyoshi, Tokiko Watanabe, Yoshihiro Kawaoka, Hiroaki Kitano:
  systemsDock: a web server for network pharmacology-based prediction and analysis. W507-W513
• 
  Duangrudee Tanramluk, Lalita Narupiyakul, Ruj Akavipat, Sungsam Gong, Varodom Charoensawan:
  MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein-ligand fragment interaction, pathways and SNPs. W514-W521
• 
  Agnieszka Obarska-Kosinska, Alfredo Iacoangeli, Rosalba Lepore, Anna Tramontano:
  PepComposer: computational design of peptides binding to a given protein surface. W522-W528
• 
  Diego Alonso-López, Miguel A. Gutiérrez, Katia P. Lopes, Carlos Prieto, Rodrigo Santamaría, Javier De Las Rivas:
  APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. W529-W535
• 
  Yuval Sedan, Orly Marcu, Sergey Lyskov, Ora Schueler-Furman:
  Peptiderive server: derive peptide inhibitors from protein-protein interactions. W536-W541
• 
  Jinchao Yu, Marek Vavrusa, Jessica Andreani, Julien Rey, Pierre Tufféry, Raphaël Guérois:
  InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information. W542-W549
• 
  Ge-Fei Hao, Wen Jiang, Yuan-Nong Ye, Feng-Xu Wu, Xiao-Lei Zhu, Feng-Biao Guo, Guangfu Yang:
  ACFIS: a web server for fragment-based drug discovery. W550-W556
• 
  Douglas E. V. Pires, David B. Ascher:
  CSM-lig: a web server for assessing and comparing protein-small molecule affinities. W557-W561
• 
  Zhichao Miao, Eric Westhof:
  RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database. W562-W567
• 
  Inbal Paz, Efrat Kligun, Barak Bengad, Yael Mandel-Gutfreund:
  BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins. W568-W574
• 
  T. Mamie Lih, Wai-Kok Choong, Chen-Chun Chen, Cheng-Wei Cheng, Hsin-Nan Lin, Ching-Tai Chen, Hui-Yin Chang, Wen-Lian Hsu, Ting-Yi Sung:
  MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification. W575-W580
• 
  Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer:
  DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. W581-W586
• 
  Andrew M. Roberts, Aaron K. Wong, Ian Fisk, Olga G. Troyanskaya:
  GIANT API: an application programming interface for functional genomics. W587-W592