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ORCIDNucleic Acids Research, Volume 50
Volume 50, Number W1, July 2022
- Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022. 1-3
- Polina Belokopytova, Emil Viesná, Mateusz Chilinski
, Yifeng Qi, Hossein Salari, Marco Di Stefano, Andrea Esposito, Mattia Conte, Andrea Maria Chiariello, Vladimir B. Teif, Dariusz Plewczynski, Bin Zhang, Daniel Jost, Veniamin Fishman:
3DGenBench: a web-server to benchmark computational models for 3D Genomics. 4-12 - Jake E. McGreig, Hannah Uri, Magdalena Antczak, Michael J. E. Sternberg, Martin Michaelis, Mark N. Wass:
3DLigandSite: structure-based prediction of protein-ligand binding sites. 13-20 - Chih-Chieh Chen, Yen-Yi Liu, Ya-Chu Yang, Chu-Yi Hsu:
5NosoAE: a web server for nosocomial bacterial antibiogram investigation and epidemiology survey. 21-28 - René Staritzbichler, Emily Yaklich, Edoardo Sarti, Nikola Ristic, Peter W. Hildebrand, Lucy R. Forrest:
AlignMe: an update of the web server for alignment of membrane protein sequences. 29-35 - Minh N. Nguyen, Nora L. Krutz, Vachiranee Limviphuvadh, Andreas L. Lopata, G. Frank Gerberick, Sebastian Maurer-Stroh:
AllerCatPro 2.0: a web server for predicting protein allergenicity potential. 36-43 - Wanda Niemyska, Pawel Rubach, Bartosz Ambrozy Gren, Mai Lan Nguyen, Wojciech Garstka, Fernando Bruno da Silva, Eric J. Rawdon, Joanna I. Sulkowska:
AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods. 44-50 - Alexandr Boytsov, Sergey Abramov, Ariuna Z. Aiusheeva, Alexandra M. Kasianova, Eugene Baulin, Ivan A. Kuznetsov, Yurii s Aulchenko, Semyon Kolmykov, Ivan S. Yevshin, Fedor A. Kolpakov, Ilya E. Vorontsov, Vsevolod J. Makeev, Ivan V. Kulakovskiy:
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs. 51-56 - Zhu Liu, Tremayne Mushayahama, Bryan Queme, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Paul D. Thomas, Huaiyu Mi:
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation. 57-65 - Qifan Zeng, Baojun Zhao, Hao Wang, Mengqiu Wang, Mingxuan Teng, Jingjie Hu, Zhenmin Bao, Yangfan Wang:
Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture. 66-74 - Yi Yang, Yufeng Mao, Ruoyu Wang, Haoran Li, Ye Liu, Haijiao Cheng, Zhenkun Shi, Yu Wang, Meng Wang, Ping Zheng, Xiaoping Liao, Hongwu Ma:
AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms. 75-82 - Robin Steinhaus, Felix Boschann, Melanie Vogel, Björn Fischer-Zirnsak, Dominik Seelow:
AutozygosityMapper: Identification of disease-mutations in consanguineous families. 83-89 - András Micsonai, Éva Moussong, Frank Wien, Eszter Boros, Henrietta Vadászi, Nikoletta Murvai, Young-Ho Lee, Tamás Molnár, Matthieu Réfrégiers, Yuji Goto, Ágnes Tantos, József Kardos:
BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy. 90-98 - Genis Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluis Gelpí:
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. 99-107 - Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. 108-114 - David S. Wishart, Siyang Tian, Dana Allen, Eponine Oler, Harrison Peters, Vicki W. Lui, Vasuk Gautam, Yannick Djoumbou Feunang, Russell Greiner, Thomas O. Metz:
BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products. 115-123 - Fedor A. Kolpakov, Ilya R. Akberdin, Ilya Kiselev, Semyon Kolmykov, Yury V. Kondrakhin, Mikhail Kulyashov, Elena Kutumova, Sergey Pintus, Anna Ryabova, Ruslan N. Sharipov, Ivan S. Yevshin, Sergey Zhatchenko, Alexander E. Kel:
BioUML - towards a universal research platform. 124-131 - Georges P. Schmartz, Pascal Hirsch, Jérémy Amand, Jan Dastbaz, Tobias Fehlmann, Fabian Kern, Rolf Müller, Andreas Keller:
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning. 132-137 - Michael Hartung, Elisa Anastasi, Zeinab M. Mamdouh, Cristian Nogales, Harald H. H. W. Schmidt, Jan Baumbach, Olga I. Zolotareva, Markus List:
Cancer driver drug interaction explorer. 138-144 - Antonin Kunka, David Lacko, Jan Stourac, Jirí Damborský, Zbynek Prokop, Stanislav Mazurenko:
CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. 145-151 - David Kuták, Lucas Melo, Fabian Schroeder, Zoe Jelic-Matosevic, Natalie Mutter, Branimir Bertosa, Ivan Barisic:
CATANA: an online modelling environment for proteins and nucleic acid nanostructures. 152-158 - Yang Liu, Xiaocong Yang, Jianhong Gan, Shuang Chen, Zhixiong Xiao, Yang Cao:
CB-Dock2: improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting. 159-164 - Fei Wang, Dana Allen, Siyang Tian, Eponine Oler, Vasuk Gautam, Russell Greiner, Thomas O. Metz, David S. Wishart:
CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. 165-174 - Zhaonan Zou, Tazro Ohta, Fumihito Miura, Shinya Oki:
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. 175-182 - Muntaha Samad, Forest Agostinelli, Tomoki Sato, Kohei Shimaji, Pierre Baldi:
CircadiOmics: circadian omic web portal. 183-190 - Vasileios Konstantakos, Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras:
CRISPRedict: a CRISPR-Cas9 web tool for interpretable efficiency predictions. 191-198 - Thach Nguyen, Haribaskar Ramachandran, Soraia Martins, Jean Krutmann, Andrea Rossi:
Identification of genome edited cells using CRISPRnano. 199-203 - Carlos H. M. Rodrigues, David B. Ascher:
CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. 204-209 - Liisa Holm:
Dali server: structural unification of protein families. 210-215 - Brad T. Sherman, Ming Hao, Ju Qiu, Xiaoli Jiao, Michael W. Baseler, H. Clifford Lane, Tomozumi Imamichi, Weizhong Chang:
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). 216-221 - Ludovica Montanucci, Emidio Capriotti, Giovanni Birolo, Silvia Benevenuta, Corrado Pancotti, Dennis Lal, Piero Fariselli:
DDGun: an untrained predictor of protein stability changes upon amino acid variants. 222-227 - Vineet Thumuluri, José Juan Almagro Armenteros, Alexander Rosenberg Johansen, Henrik Nielsen, Ole Winther:
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models. 228-234 - Xiaogen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Guijun Zhang, Yang Zhang:
DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. 235-245 - Fei Ji, Gracia Bonilla, Rustem Krykbaev, Gary Ruvkun, Yuval Tabach, Ruslan I. Sadreyev:
DEPCOD: a tool to detect and visualize co-evolution of protein domains. 246-253 - Suyeon Wy, Daehong Kwon, Kisang Kwon, Jaebum Kim:
DLEB: a web application for building deep learning models in biological research. 254-260 - Razieh Mohammadi-Arani, Fatemeh Javadi-Zarnaghi, Pietro Boccaletto, Janusz M. Bujnicki, Almudena Ponce-Salvatierra:
DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes. 261-265 - Christopher P. Jurich, Amir Brivanlou, Silvi Rouskin, Joseph D. Yesselman:
Web-based platform for analysis of RNA folding from high throughput chemical probing data. 266-271 - Aleksandr Ianevski, Ronja M. Simonsen, Vegard Myhre, Tanel Tenson, Valentyn Oksenych, Magnar Bjørås, Denis E. Kainov:
DrugVirus.info 2.0: an integrative data portal for broad-spectrum antivirals (BSA) and BSA-containing drug combinations (BCCs). 272-275 - Fábio Madeira, Matt Pearce, Adrian R. N. Tivey, Prasad Basutkar, Joon Lee, Ossama Edbali, Nandana Madhusoodanan, Anton Kolesnikov, Rodrigo Lopez:
Search and sequence analysis tools services from EMBL-EBI in 2022. 276-279 - Michael Soutschek, Tomás Germade, Pierre-Luc Germain, Gerhard Schratt:
enrichMiR predicts functionally relevant microRNAs based on target collections. 280-289 - Li Tang, Zhizhou Zhong, Yisheng Lin, Yifei Yang, Jun Wang, James F. Martin, Min Li:
EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions. 290-297 - Zhitao Mao, Ruoyu Wang, Haoran Li, Yixin Huang, Qiang Zhang, Xiaoping Liao, Hongwu Ma:
ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database. 298-304 - Marc-André Legault, Louis-Philippe Lemieux Perreault, Jean-Claude Tardif, Marie-Pierre Dubé:
ExPheWas: a platform for cis-Mendelian randomization and gene-based association scans. 305-311 - Xian Liu, Kaikun Xu, Xin Tao, Ronghua Yin, Guangming Ren, Miao Yu, Changyan Li, Hui Chen, Ke Zhao, Shensi Xiang, Huiying Gao, Xiaochen Bo, Cheng Chang, Xiaoming Yang:
ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data. 312-321 - Robin Steinhaus, Peter N. Robinson, Dominik Seelow:
FABIAN-variant: predicting the effects of DNA variants on transcription factor binding. 322-329 - Anne de Jong, Oscar P. Kuipers, Jan Kok:
FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes. 330-336 - András Hatos, Silvio C. E. Tosatto, Michele Vendruscolo, Mónika Fuxreiter:
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins. 337-344 - Enis Afgan, Anton Nekrutenko, Björn A. Grüning, Daniel J. Blankenberg, Jeremy Goecks, Michael C. Schatz, Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. 345-351 - Jorge Botas, Álvaro Rodríguez del Río, Joaquín Giner-Lamia, Jaime Huerta-Cepas:
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective. 352-357 - Christopher A. Mancuso, Patrick S. Bills, Douglas Krum, Jacob Newsted, Renming Liu, Arjun Krishnan:
GenePlexus: a web-server for gene discovery using network-based machine learning. 358-366 - Guy P. Hunt, Luigi Grassi, Rafael Henkin, Fabrizio Smeraldi, Thomas P. Spargo, Renata Kabiljo, Sulev Koks, Zina M. Ibrahim, Richard J. B. Dobson, Ammar Al-Chalabi, Michael R. Barnes, Alfredo Iacoangeli:
GEOexplorer: a webserver for gene expression analysis and visualisation. 367-374 - Nur Syatila Abdul Ghani, Reeki Emrizal, Sabrina Mohamed Moffit, Hazrina Yusof Hamdani, Effirul Ikhwan Ramlan, Mohd Firdaus Raih:
GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA. 375-383 - Erich R. Kuechler, Matthew Jacobson, Thibault Mayor, Jörg Gsponer:
GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents. 384-391 - Charles Abreu Santana, Sandro C. Izidoro, Raquel Cardoso de Melo Minardi, Jonathan D. Tyzack, António J. M. Ribeiro, Douglas E. V. Pires, Janet M. Thornton, Sabrina de Azevedo Silveira:
GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs. 392-397 - Deniz Seçilmis, Thomas Hillerton, Erik L. L. Sonnhammer:
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods. 398-404 - Wanshan Ning, Yuxiang Wei, Letian Gao, Cheng Han, Yujie Gou, Shanshan Fu, Dan Liu, Chi Zhang, Xinhe Huang, Sicheng Wu, Di Peng, Chenwei Wang, Yu Xue:
HemI 2.0: an online service for heatmap illustration. 405-411 - Francesco Oteri, Edoardo Sarti, Francesca Nadalin, Alessandra Carbone:
iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families. 412-419 - Yubin Xie, Huiqin Li, Xiaotong Luo, Hongyu Li, Qiuyuan Gao, Luowanyue Zhang, Yuyan Teng, Qi Zhao, Zhixiang Zuo, Jian Ren:
IBS 2.0: an upgraded illustrator for the visualization of biological sequences. 420-426 - Andrew Jiang, Klaus Lehnert, Linya You, Russell G. Snell:
ICARUS, an interactive web server for single cell RNA-seq analysis. 427-433 - Zhen Chen, Xuhan Liu, Pei Zhao, Chen Li, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Chris Bain, Robin B. Gasser, Junzhou Li, Zuoren Yang, Xin Gao, Lukasz A. Kurgan, Jiangning Song:
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. 434-447 - Dmitri S. Pavlichin, Hojoon Lee, Stephanie U. Greer, Susan M. Grimes, Tsachy Weissman, Hanlee P. Ji:
KmerKeys: a web resource for searching indexed genome assemblies and variants. 448-453 - Wei Zheng, Qiqige Wuyun, Xiaogen Zhou, Yang Li, Peter L. Freddolino, Yang Zhang:
LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. 454-464 - Joan Planas-Iglesias, Filip Opálený, Pavol Ulbrich, Jan Stourac, Zainab K. Sanusi, Gaspar R. P. Pinto, Andrea Schenkmayerova, Jan Byska, Jirí Damborský, Barbora Kozlíková, David Bednar:
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. 465-473 - Aleksandra E. Badaczewska-Dawid, Chandran Nithin, Karol Wroblewski, Mateusz Kurcinski, Sebastian Kmiecik:
MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes. 474-482 - Michelle Kampfrath, René Staritzbichler, Guillermo Pérez Hernández, Alexander S. Rose, Johanna K. S. Tiemann, Gerik Scheuermann, Daniel Wiegreffe, Peter W. Hildebrand:
MDsrv: visual sharing and analysis of molecular dynamics simulations. 483-489 - Fabio Marchiano, Margaux Haering, Bianca Hermine Habermann:
The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context. 490-499 - Shu-Cheng Liu, Yan-Ru Ju, Chin Lung Lu:
Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes. 500-509 - Magnus Haraldson Høie, Erik Nicolas Kiehl, Bent Petersen, Morten Nielsen, Ole Winther, Henrik Nielsen, Jeppe Hallgren, Paolo Marcatili:
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning. 510-515 - Caroline Vernette, Julien Lecubin, Pablo Sánchez, Silvia G. Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Gabriel Gorsky, Lionel Guidi, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels-Lewis, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole Poulton, Stephane Pesant, Christian Sardet, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker, Tom O. Delmont, Eric Pelletier, Magali Lescot:
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. 516-526 - Guangyan Zhou, Zhiqiang Pang, Yao Lu, Jessica Ewald, Jianguo Xia:
OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics. 527-533 - Ivan S. Ilnitskiy, Anastasia Zharikova, Andrey Mironov:
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins. 534-540 - Leighton J. Payne, Sean Meaden, Mario R. Mestre, Chris Palmer, Nicolás Toro, Peter C. Fineran, Simon A. Jackson:
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. 541-550 - Tianyuan Liu, Pedro Salguero, Marko Petek, Carlos Martínez-Mira, Leandro Balzano-Nogueira, Ziva Ramsak, Lauren McIntyre, Kristina Gruden, Sonia Tarazona, Ana Conesa:
PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases. 551-559 - Mirko Schmitz, Anne Schultze, Raimonds Vanags, Karsten Voigt, Barbara Di Ventura, Mehmet Ali Öztürk:
patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures. 560-567 - Chao Xue, Lin Jiang, Miao Zhou, Qihan Long, Ying Chen, Xiangyi Li, Wenjie Peng, Qi Yang, Miao-Xin Li:
PCGA: a comprehensive web server for phenotype-cell-gene association analysis. 568-576 - Ziqi Deng, Jorge Botas, Carlos P. Cantalapiedra, Ana Hernández-Plaza, Jordi Burguet-Castell, Jaime Huerta-Cepas:
PhyloCloud: an online platform for making sense of phylogenomic data. 577-582 - Hai Fang:
PiER: web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions. 583-592 - David Jakubec, Petr Skoda, Radoslav Krivák, Marian Novotny, David Hoksza:
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures. 593-597 - Marin Matic, Gurdeep Singh, Francesco Carli, Natalia De Oliveira Rosa, Pasquale Miglionico, Lorenzo Magni, J. Silvio Gutkind, Robert B. Russell, Asuka Inoue, Francesco Raimondi:
PRECOGx: exploring GPCR signaling mechanisms with deep protein representations. 598-610 - Katrin Schöning-Stierand, Konrad Diedrich, Christiane Ehrt, Florian Flachsenberg, Joel Graef, Jochen Sieg, Patrick Penner, Martin Poppinga, Annett Ungethüm, Matthias Rarey:
ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. 611-615 - Peng-Hsuan Li, Ting-Fu Chen, Jheng-Ying Yu, Shang-Hung Shih, Chan-Hung Su, Yin-Hung Lin, Huai-Kuang Tsai, Hsueh-Fen Juan, Chien-Yu Chen, Jia-Hsin Huang:
pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature. 616-622 - Yannis Nevers, Tamsin E. M. Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codó, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Pilizota, Cristina Guijarro-Clarke, Adrian M. Altenhoff, Elspeth A. Bruford, Christophe Dessimoz, Ingo Ebersberger, David M. Emms, Toni Gabaldón, Natasha Glover, Yanhui Hu, Wataru Iwasaki, Odile Lecompte, Benjamin Linard, María J. Martín, David S. Roos, Erik Sonhammer, Paul D. Thomas, David Thybert, Klaas Vandepoele, Salvador Capella-Gutiérrez, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas, Dmitry Repchevsky, Vicky Sundesha, Erik L. L. Sonnhammer:
The Quest for Orthologs orthology benchmark service in 2022. 623-632 - Lei Zheng, Dongyang Liu, Yuan Alex Li, Siqi Yang, Yuchao Liang, Yongqiang Xing, Yongchun Zuo:
RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets. 633-638 - Zoe Weiss, Saurja Dasgupta:
REVERSE: a user-friendly web server for analyzing next-generation sequencing data from in vitro selection/evolution experiments. 639-650 - Damiano Clementel, Alessio Del Conte, Alexander Miguel Monzon, Giorgia F. Camagni, Giovanni Minervini, Damiano Piovesan, Silvio C. E. Tosatto:
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles. 651-656 - Marcin Magnus:
rna-tools.online: a Swiss army knife for RNA 3D structure modeling workflow. 657-662 - Kamil Luwanski, Vladyslav Hlushchenko, Mariusz Popenda, Tomasz Zok, Joanna Sarzynska, Daniil Martsich, Marta Szachniuk, Maciej Antczak:
RNAspider: a webserver to analyze entanglements in RNA 3D structures. 663-669 - Walter Santana-Garcia, Jaime Abraham Castro-Mondragón, Mónica Padilla-Gálvez, Nga Thi Thuy Nguyen, Ana Elizondo-Salas, Najla Ksouri, François Gerbes, Denis Thieffry, Pierre Vincens, Bruno Contreras-Moreira, Jacques van Helden, Morgane Thomas-Chollier, Alejandra Medina-Rivera:
RSAT 2022: regulatory sequence analysis tools. 670-676 - Robin Steinhaus, Sebastian Proft, Evelyn Seelow, Tobias Schalau, Peter N. Robinson, Dominik Seelow:
Deep phenotyping: symptom annotation made simple with SAMS. 677-681 - Mehmet Direnç Mungan, Theresa Anisja Harbig, Naybel Hernandez Perez, Simone Edenhart, Evi Stegmann, Kay Nieselt, Nadine Ziemert:
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. 682-689 - Mariia Emelianova, Anastasiia N. Gainullina, Nikolay Poperechnyi, Alexander A. Loboda, Maxim N. Artyomov, Alexey A. Sergushichev:
Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks. 690-696 - John Erol Evangelista, Daniel J. B. Clarke, Zhuorui Xie, Alexander Lachmann, Minji Jeon, Kerwin Chen, Kathleen M. Jagodnik, Sherry L. Jenkins, Maxim V. Kuleshov, Megan L. Wojciechowicz, Stephan C. Schürer, Mario Medvedovic, Avi Ma'ayan:
SigCom LINCS: data and metadata search engine for a million gene expression signatures. 697-709 - Ernesto Aparicio-Puerta, Cristina Gómez-Martín, Stavros Giannoukakos, José María Medina, Chantal Scheepbouwer, Adrián García-Moreno, Pedro Carmona-Saez, Bastian Fromm, Michiel Pegtel, Andreas Keller, Juan Antonio Marchal, Michael Hackenberg:
sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. 710-717 - Joanne Watson, Michael Smith, Chiara Francavilla, Jean-Marc Schwartz:
SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment. 718-725 - Kathleen Gallo, Andrean Goede, Robert Preissner, Björn-Oliver Gohlke:
SuperPred 3.0: drug classification and target prediction - a machine learning approach. 726-731 - Gabriel Cretin, Tatiana Galochkina, Yann Vander Meersche, Alexandre G. de Brevern, Guillaume Postic, Jean-Christophe Gelly:
SWORD2: hierarchical analysis of protein 3D structures. 732-738 - Aleksandr Ianevski, Anil K. Giri, Tero Aittokallio:
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples. 739-743 - Barbara Poszewiecka, Victor Murcia Pienkowski, Karol Nowosad, Jérôme D. Robin, Krzysztof Gogolewski, Anna Gambin:
TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure. 744-752 - Dominique Sydow, Jaime Rodríguez-Guerra, Talia B. Kimber, David Schaller, Corey J. Taylor, Yonghui Chen, Mareike Leja, Sakshi Misra, Michele Wichmann, Armin Ariamajd, Andrea Volkamer:
TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research. 753-760 - Li Chen, Tianjian Chen, Ya Zhang, Haichen Lin, Ruihan Wang, Yihang Wang,