Journal: Nucleic Acids Research

Volume 49, Issue Webserver-Issue

1 -- 4. Nucleic Acids Research web server issue 2021
5 -- 14Guo-Li Xiong, Zhenxing Wu, Jia-Cai Yi, Li Fu, Zhi-Jiang Yang, Chang-Yu Hsieh, Mingzhu Yin, Xiangxiang Zeng, Chengkun Wu, Ai-Ping Lu, Xiang Chen, Tingjun Hou, Dong-Sheng Cao 0001. ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties
15 -- 20Jirí Vymetal, David Jakubec, Jakub Galgonek, Jirí Vondrásek. Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures
21 -- 28Véronique Geoffroy, Thomas Guignard, Arnaud Kress, Jean-Baptiste Gaillard, Tor Solli-Nowlan, Audrey Schalk, Vincent Gatinois, Hélène Dollfus, Sophie Scheidecker, Jean Muller. AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis
29 -- 35Kai Blin, Simon Shaw, Alexander M. Kloosterman, Zachary Charlop-Powers, Gilles P. van Wezel, Marnix H. Medema, Tilmann Weber. antiSMASH 6.0: improving cluster detection and comparison capabilities
36 -- 45Evangelos Karatzas, Fotis A. Baltoumas, Nikolaos A. Panayiotou, Reinhard Schneider 0002, Georgios A. Pavlopoulos. Arena3Dweb: interactive 3D visualization of multilayered networks
46 -- 51Tobias Fehlmann, Fabian Kern, Pascal Hirsch, Robin Steinhaus, Dominik Seelow, Andreas Keller. Aviator: a web service for monitoring the availability of web services
52 -- 59Luciano Porto Kagami, Gabriele Orlando, Daniele Raimondi, Francois Ancien, Bhawna Dixit, Jose Gavaldá-García, Pathmanaban Ramasamy, Joel Roca-Martínez, Konstantina Tzavella, Wim F. Vranken. b2bTools: online predictions for protein biophysical features and their conservation
60 -- 66Davide Baldazzi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio. BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation
67 -- 71Andrea Guarracino, Gerardo Pepe, Francesco Ballesio, Marta Adinolfi, Marco Pietrosanto, Elisa Sangiovanni, Ilio Vitale, Gabriele Ausiello, Manuela Helmer-Citterich. BRIO: a web server for RNA sequence and structure motif scan
72 -- 79Alexandros Armaos, Alessio Colantoni, Gabriele Proietti, Jakob Rupert, Gian Gaetano Tartaglia. omics v2.0: going deeper and wider in the prediction of protein-RNA interactions
80 -- 85Irepan Salvador-Martínez, Marco Grillo, Michalis Averof, Maximilian J. Telford. CeLaVi: an interactive cell lineage visualization tool
86 -- 92Dariusz Brzezinski, Przemyslaw J. Porebski, Marcin Kowiel, Joanna M. Macnar, Wladek Minor. Recognizing and validating ligands with CheckMyBlob
93 -- 103Francisco Requena, Hamza Hadj Abdallah, Alejandro García, Patrick Nitschké, Sergi Romana, Valérie Malan, Antonio Rausell. CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients
104 -- 113Jeffrey Molendijk, Marcus M. Seldin, Benjamin L. Parker. CoffeeProt: an online tool for correlation and functional enrichment of systems genetics data
114 -- 124Hung Nguyen, Duc Tran, Jonathan M. Galazka, Sylvain V. Costes, Afshin Beheshti, Juli Petereit, Sorin Draghici, Tin Nguyen 0001. CPA: a web-based platform for consensus pathway analysis and interactive visualization
125 -- 130Omer S. Alkhnbashi, Alexander Mitrofanov, Robson Bonidia, Martin Raden, Van Dinh Tran, Florian Eggenhofer, Shiraz A. Shah, Ekrem Öztürk, Victor Alexandre Padilha, Danilo Sipoli Sanches, André C. P. L. F. de Carvalho, Rolf Backofen. <tt>CRISPRloci: </tt> comprehensive and accurate annotation of CRISPR-Cas systems
131 -- 139Guangsheng Pei, Ruifeng Hu 0002, Peilin Jia, Zhongming Zhao. DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner
140 -- 146Maxat Kulmanov, Fernando Zhapa-Camacho, Robert Hoehndorf. DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web
147 -- 152Md Hossain Shuvo, Muhammad Gulfam, Debswapna Bhattacharya. DeepRefiner: high-accuracy protein structure refinement by deep network calibration
153 -- 161Jiajing Hu, Rosalba Lepore, Richard J. B. Dobson, Ammar Al-Chalabi, Daniel Bean, Alfredo Iacoangeli. DGLinker: flexible knowledge-graph prediction of disease-gene associations
162 -- 168Shani T. Gal-Oz, Nimrod Haiat, Dana Eliyahu, Guy Shani, Tal Shay. DoChaP: the domain change presenter
169 -- 173Pascal Schläpfer, Devang Mehta, Cameron Ridderikhoff, R. Glen Uhrig. DomainViz: intuitive visualization of consensus domain distributions across groups of proteins
174 -- 184Shuyu Zheng, Jehad Aldahdooh, Tolou Shadbahr, Yinyin Wang, Dalal Aldahdooh, Jie Bao, Wenyu Wang, Jing Tang 0002. DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal
185 -- 192Marius A. Dieckmann, Sebastian Beyvers, Rudel Christian Nkouamedjo-Fankep, Patrick Harald Georg Hanel, Lukas Jelonek, Jochen Blom, Alexander Goesmann. EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
193 -- 198Shuntaro Chiba, Kenji Rowel Q. Lim, Narin Sheri, Saeed Anwar, Esra Erkut, Md Nur Ahad Shah, Tejal Aslesh, Stanley Woo, Omar Sheikh, Rika Maruyama, Hiroaki Takano, Katsuhiko Kunitake, William Duddy, Yasushi Okuno, Yoshitsugu Aoki, Toshifumi Yokota. eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping
199 -- 206Pietro di Lena, Claudia Sala, Christine Nardini. Estimage: a webserver hub for the computation of methylation age
207 -- 215Xuanjin Cheng, Junran Yan, Yongxing Liu, Jiahe Wang, Stefan Taubert. eVITTA: a web-based visualization and inference toolbox for transcriptome analysis
216 -- 227Severine Duvaud, Chiara Gabella, Frédérique Lisacek, Heinz Stockinger, Vassilios Ioannidis, Christine Durinx. Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users
228 -- 236Shuai Zeng, Ziting Mao, Yijie Ren, Duolin Wang, Dong Xu 0002, Trupti Joshi. G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers
237 -- 241Taeyong Park, Jonghun Won, Minkyung Baek, Chaok Seok. ab initio docking
242 -- 246Chenwei Li, Zefang Tang, Wenjie Zhang, Zhaochen Ye, Fenglin Liu. GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA
247 -- 256Przemyslaw Miszta, Pawel Pasznik, Szymon Niewieczerzal, Jakub Jakowiecki, Slawomir Filipek. GPCRsignal: webserver for analysis of the interface between G-protein-coupled receptors and their effector proteins by dynamics and mutations
257 -- 262Heyuan Zeng, Jinbiao Zhang, Gabriel A. Preising, Tobias Rubel, Pramesh Singh, Anna M. Ritz. Graphery: interactive tutorials for biological network algorithms
263 -- 270Victòria Pascal Andreu, Jorge Roel-Touris, Dylan Dodd, Michael A. Fischbach, Marnix H. Medema. The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota
271 -- 276Muhammad Arif, Cheng Zhang, Xiangyu Li, Cem Güngör, Bugra Çakmak, Metin Arslantürk, Abdellah Tebani, Berkay Özcan, Oguzhan Subas, Wenyu Zhou, Brian Piening, Hasan Turkez, Linn Fagerberg, Nathan Price, Leroy Hood, Michael Snyder, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu. iNetModels 2.0: an interactive visualization and database of multi-omics data
277 -- 284Chloé Quignot, Guillaume Postic, Hélène Bret, Julien Rey, Pierre Granger, Samuel Murail, Pablo Chacón, Jessica Andreani, Pierre Tufféry, Raphaël Guérois. InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps
285 -- 292Lukasz P. Kozlowski. Ka dissociation constants
293 -- 296Ivica Letunic, Peer Bork. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
297 -- 303Gábor Erdös 0002, Mátyás Pajkos, Zsuzsanna Dosztányi. IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation
304 -- 316Maxim V. Kuleshov, Zhuorui Xie, Alexandra B. K. London, Janice Yang, John Erol Evangelista, Alexander Lachmann, Ingrid Shu, Denis Torre, Avi Ma'ayan. KEA3: improved kinase enrichment analysis via data integration
317 -- 325Dechao Bu, Haitao Luo, Peipei Huo, ZhiHao Wang, Shan Zhang, Zihao He, Yang Wu, Lianhe Zhao, Jingjia Liu, Jincheng Guo, Shuangsang Fang, Wanchen Cao, Lan Yi, Yi Zhao, Lei Kong. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis
326 -- 335Luca Pinzi, Annachiara Tinivella, Luca Gagliardelli, Domenico Beneventano, Giulio Rastelli. LigAdvisor: a versatile and user-friendly web-platform for drug design
336 -- 345Wen-Jen Lin, Pei-Chun Shen, Hsiu-Cheng Liu, Yi-Chun Cho, Min-Kung Hsu, I-Chen Lin, Fang-Hsin Chen, Juan-Cheng Yang, Wen-Lung Ma, Wei-Chung Cheng. LipidSig: a web-based tool for lipidomic data analysis
346 -- 351Ahmed Mohamed, Michelle M. Hill. LipidSuite: interactive web server for lipidomics differential and enrichment analysis
352 -- 358Alexis Allot, Kyubum Lee, Qingyu Chen 0001, Ling Luo 0001, Zhiyong Lu. LitSuggest: a web-based system for literature recommendation and curation using machine learning
359 -- 365Charles Christoffer, Siyang Chen, Vijay Bharadwaj, Tunde Aderinwale, Vidhur Kumar, Matin Hormati, Daisuke Kihara. LZerD webserver for pairwise and multiple protein-protein docking
366 -- 374Juan Carlos González-Sánchez, Mustafa F. R. Ibrahim, Ivo C. Leist, Kyle R. Weise, Robert B. Russell. Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants
375 -- 387Jessica Ding, Montgomery Blencowe, Thien Nghiem, Sung Min Ha, Yen-Wei Chen, Gaoyan Li, Xia Yang. Mergeomics 2.0: a web server for multi-omics data integration to elucidate disease networks and predict therapeutics
388 -- 396Zhiqiang Pang, Jasmine Chong, Guangyan Zhou, David A. de Lima Morais, Le Chang, Michel Barrette, Carol Gauthier, Pierre-Étienne Jacques, Shuzhao Li, Jianguo Xia. MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights
397 -- 408Tobias Fehlmann, Fabian Kern, Omar Laham, Christina Backes, Jeffrey Solomon, Pascal Hirsch, Carsten Volz, Rolf Müller 0002, Andreas Keller. miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale
409 -- 416Fabian Kern, Ernesto Aparicio-Puerta, Yongping Li, Tobias Fehlmann, Tim Kehl, Viktoria Wagner, Kamalika Ray, Nicole Ludwig 0001, Hans-Peter Lenhof, Eckart Meese, Andreas Keller. miRTargetLink 2.0 - interactive miRNA target gene and target pathway networks
417 -- 424Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher. mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions
425 -- 430Liam J. McGuffin, Fahd M. F. Aldowsari, Shuaa M. A Alharbi, Recep Adiyaman. ModFOLD8: accurate global and local quality estimates for 3D protein models
431 -- 437David Sehnal, Sebastian Bittrich, Mandar S. Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K. Burley, Jaroslav Koca, Alexander S. Rose. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
438 -- 445Michael Silk, Douglas E. V. Pires, Carlos H. M. Rodrigues, Elston N. D'souza, Moshe Olshansky, Natalie Thorne, David B. Ascher. MTR3D: identifying regions within protein tertiary structures under purifying selection
446 -- 451Robin Steinhaus, Sebastian Proft, Markus Schuelke, David N. Cooper, Jana Marie Schwarz, Dominik Seelow. MutationTaster2021
452 -- 458Riccardo Vicedomini, Clémence Blachon, Francesco Oteri, Alessandra Carbone. MyCLADE: a multi-source domain annotation server for sequence functional exploration
459 -- 468Yuwei Zhang, Dechao Bu, Peipei Huo, ZhiHao Wang, Hao Rong, Yanguo Li, Jingjia Liu, Meng Ye, Yang Wu, Zheng Jiang, Qi Liao, Yi Zhao. ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs
469 -- 475Shuwei Yao, Ronghui You, Shaojun Wang, Yi Xiong, Xiaodi Huang, Shanfeng Zhu. NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information
476 -- 482Guangyan Zhou, Jessica Ewald, Jianguo Xia. OmicsAnalyst: a comprehensive web-based platform for visual analytics of multi-omics data
483 -- 490Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang 0001. OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions
491 -- 498Erik Poppleton, Roger Romero, Aatmik Mallya, Lorenzo Rovigatti, Petr Sulc. OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
499 -- 504Gue-Ho Hwang, You Kyeong Jeong, Omer Habib, Sung-Ah Hong, Kayeong Lim, Jin-Soo Kim, Sangsu Bae. PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing
505 -- 509Mads Valdemar Anderson, Jakob Haldrup, Emil Aagaard Thomsen, Jonas holst Wolff, Jacob giehm Mikkelsen. pegIT - a web-based design tool for prime editing
510 -- 515Muhammad Farhan Khalid, Kanzal Iman, Amna Ghafoor, Mujtaba Saboor, Ahsan Ali, Urwa Muaz, Abdul Rehman Basharat, Taha Tahir, Muhammad Abubakar, Momina Amer Akhter, Waqar Nabi, Wim Vanderbauwhede, Fayyaz Ahmad, Bilal Wajid, Safee Ullah Chaudhary. PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics
516 -- 522Matthew J. McGuffie, Jeffrey E. Barrick. pLannotate: engineered plasmid annotation
523 -- 529Hu Zhao, Zhuo Tu, Yinmeng Liu, Zhanxiang Zong, Jiacheng Li, Hao Liu, Feng Xiong, Jinling Zhan, Xuehai Hu, Weibo Xie. PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants
530 -- 534Melissa F. Adasme, Katja L. Linnemann, Sarah Naomi Bolz, Florian Kaiser, Sebastian Salentin, V. Joachim Haupt, Michael Schroeder. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA
535 -- 540Michael Bernhofer, Christian Dallago, Timothy Karl, Venkata P. Satagopam, Michael Heinzinger, Maria Littmann, Tobias Olenyi, Jiajun Qiu, Konstantin Schütze, Guy Yachdav, Haim Ashkenazy, Nir Ben-Tal, Yana Bromberg, Tatyana Goldberg, László Kaján, Seán I. O'Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider 0002, Burkhard Rost. PredictProtein - Predicting Protein Structure and Function for 29 Years
541 -- 543Martin Gühmann, Stefanie Reuter, Jan Hartung, Ralf Mrowka. Preselector.uni-jena.de: optimize your cloning - a resource for identifying restriction enzymes for preselection reactions
544 -- 550Besmir Sejdiu, D. Peter Tieleman. ProLint: a web-based framework for the automated data analysis and visualization of lipid-protein interactions
551 -- 558Sophia Mersmann, Léonie Strömich, Florian J. Song, Nan Wu, Francesca V. Vianello, Mauricio Barahona, Sophia N. Yaliraki. ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules
559 -- 566Noelia Ferruz, Steffen Schmidt, Birte Höcker. ProteinTools: a toolkit to analyze protein structures
567 -- 572Guillaume Postic, Jessica Andreani, Julien Marcoux, Victor Reys, Raphaël Guérois, Julien Rey, Emmanuelle Mouton-Barbosa, Yves Vandenbrouck, Sarah Cianférani, Odile Burlet-Schiltz, Gilles Labesse, Pierre Tufféry. Proteo3Dnet: a web server for the integration of structural information with interactomics data
573 -- 577Evangelos Theodorakis, Andreas N. Antonakis, Ismini Baltsavia, Georgios A. Pavlopoulos, Martina Samiotaki, Grigoris D. Amoutzias, Theodosios Theodosiou, Oreste Acuto, Georgios Efstathiou, Ioannis Iliopoulos. ProteoSign v2: a faster and evolved user-friendly online tool for statistical analyses of differential proteomics
578 -- 588Petar I. Penev, Holly M. McCann, Caeden D. Meade, Claudia Alvarez-Carreño, Aparna Maddala, Chad R. Bernier, Vasanta l Chivukula, Maria Ahmad, Burak Gulen, Aakash Sharma, Loren Dean Williams, Anton S. Petrov. ProteoVision: web server for advanced visualization of ribosomal proteins
589 -- 596Recep Adiyaman, Liam J. McGuffin. ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts
597 -- 602Bilal Shaikh, Gnaneswara Marupilla, Mike Wilson, Michael L. Blinov, Ion I. Moraru, Jonathan R. Karr. RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats
603 -- 612Niccolo Tesi, Sven van der Lee, Marc Hulsman, Henne Holstege, Marcel J. T. Reinders. snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets
613 -- 618Mark Wappett, Adam Harris, Alexander L. R. Lubbock, Ian Lobb, Simon S. McDade, Ian M. Overton. SynLeGG: analysis and visualization of multiomics data for discovery of cancer 'Achilles Heels' and gene function relationships
619 -- 623Peter W. Harrison, Rodrigo Lopez, Nadim Rahman, Stefan Gutnick Allen, Raheela Aslam, Nicola Buso, Carla Cummins, Yasmin Fathy, Eloy Felix, Mihai Glont, Suran Jayathilaka, Sandeep Kadam, Manish Kumar, Katharina b Lauer, Geetika Malhotra, Abayomi Mosaku, Ossama Edbali, Young-Mi Park, Andrew Parton, Matt Pearce, Jose Francisco Estrada pena, Joseph Rossetto, Craig Russell, Sandeep Selvakumar, Xènia Pérez Sitjà, Alexey Sokolov, Ross Thorne, Marianna Ventouratou, Peter Walter, Galabina Yordanova, Amonida Zadissa, Guy Cochrane, Niklas Blomberg, Rolf Apweiler. The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing
624 -- 632Denis Yuen, Louise Cabansay, Andrew Duncan, Gary Luu, Gregory Hogue, Charles Overbeck, Natalie Perez, Walt Shands, David Steinberg, Chaz Reid, Nneka Olunwa, Richard Hansen, Elizabeth Sheets, Ash O'farrell, Kim Cullion, Brian D. O'Connor, Benedict Paten, Lincoln Stein. The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols
633 -- 640Alexander L. R. Lubbock, Leonard A. Harris, Vito Quaranta, Darren R. Tyson, Carlos F. Lopez. Thunor: visualization and analysis of high-throughput dose-response datasets
641 -- 653Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, Erica Larschan. TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data
654 -- 661Bikash K. Bhandari, Chun Shen Lim, Paul P. Gardner. TISIGNER.com: web services for improving recombinant protein production
662 -- 670Stephen J. Kiniry, Ciara E. Judge, Audrey M. Michel, Pavel V. Baranov. Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data
671 -- 678Edison Ong, Michael F. Cooke, Anthony Huffman, Zuoshuang Xiang, Mei U. Wong, Haihe Wang, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He. Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning
679 -- 684Franziska Fritz, Robert Preissner, Priyanka Banerjee. VirtualTaste: a web server for the prediction of organoleptic properties of chemical compounds
685 -- 0René Staritzbichler, Nikola Ristic, Andrean Goede, Robert Preissner, Peter Werner Hildebrand. Voronoia 4-ever