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Nucleic Acids Research  
Volume 50 Issue W1
 
5 July 2022
 
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Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022 border= 
 
 
 
 
Web Server Issue
 
 
 
3DGenBench: a web-server to benchmark computational models for 3D Genomics border= 
 
Polina Belokopytova; Emil Viesná; Mateusz ChiliÅ"ski; Yifeng Qi ; Hossein Salari ...
 
 
3DLigandSite: structure-based prediction of protein'ligand binding sites border= 
 
Jake E McGreig; Hannah Uri; Magdalena Antczak; Michael J E Sternberg ; Martin Michaelis ...
 
 
5NosoAE: a web server for nosocomial bacterial antibiogram investigation and epidemiology survey border= 
 
Chih-Chieh Chen; Yen-Yi Liu; Ya-Chu Yang ; Chu-Yi Hsu
 
 
AlignMe: an update of the web server for alignment of membrane protein sequences 
 
René Staritzbichler; Emily Yaklich; Edoardo Sarti; Nikola Ristic ; Peter W Hildebrand ...
 
 
 
AllerCatPro 2.0: a web server for predicting protein allergenicity potential border= 
 
Minh N Nguyen; Nora L Krutz; Vachiranee Limviphuvadh; Andreas L Lopata ; G Frank Gerberick ...
 
 
AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods border= 
 
Wanda Niemyska; Pawel Rubach; Bartosz A Gren ; Mai Lan Nguyen; Wojciech Garstka ...
 
 
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs border= 
 
Alexandr Boytsov; Sergey Abramov; Ariuna Z Aiusheeva ; Alexandra M Kasianova; Eugene Baulin ...
 
 
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation border= 
 
Zhu Liu; Tremayne Mushayahama; Bryan Queme ; Dustin Ebert; Anushya Muruganujan ...
 
 
Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture border= 
 
Qifan Zeng; Baojun Zhao; Hao Wang ; Mengqiu Wang; Mingxuan Teng ...
 
 
 
AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms border= 
 
Yi Yang; Yufeng Mao; Ruoyu Wang ; Haoran Li; Ye Liu ...
 
 
AutozygosityMapper: Identification of disease-mutations in consanguineous families border= 
 
Robin Steinhaus; Felix Boschann; Melanie Vogel ; Björn Fischer-Zirnsak; Dominik Seelow
 
 
BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy border= 
 
András Micsonai; Éva Moussong; Frank Wien ; Eszter Boros; Henrietta Vadászi ...
 
 
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations border= 
 
Genís Bayarri; Pau Andrio; Adam Hospital ; Modesto Orozco; Josep Lluís Gelpí
 
 
BioSimulators: a central registry of simulation engines and services for recommending specific tools border= 
 
Bilal Shaikh; Lucian P Smith; Dan Vasilescu ; Gnaneswara Marupilla; Michael Wilson ...
 
 
BioTransformer 3.0'a web server for accurately predicting metabolic transformation products border= 
 
David S Wishart; Siyang Tian; Dana Allen ; Eponine Oler; Harrison Peters ...
 
 
BioUML'towards a universal research platform border= 
 
Fedor Kolpakov; Ilya Akberdin; Ilya Kiselev; Semyon Kolmykov ; Yury Kondrakhin ...
 
 
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning border= 
 
Georges P Schmartz; Pascal Hirsch; Jérémy Amand ; Jan Dastbaz; Tobias Fehlmann ...
 
 
Cancer driver drug interaction explorer border= 
 
Michael Hartung; Elisa Anastasi; Zeinab M Mamdouh; Cristian Nogales ; Harald H H W Schmidt ...
 
 
CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability border= 
 
Antonin Kunka; David Lacko; Jan Stourac ; Jiri Damborsky; Zbynek Prokop ...
 
 
CATANA: an online modelling environment for proteins and nucleic acid nanostructures border= 
 
David KuÅ¥ák; Lucas Melo; Fabian Schroeder ; Zoe Jelic-MatoÅ¡ević; Natalie Mutter ...
 
 
CB-Dock2: improved protein'ligand blind docking by integrating cavity detection, docking and homologous template fitting border= 
 
Yang Liu; Xiaocong Yang; Jianhong Gan ; Shuang Chen; Zhi-Xiong Xiao ...
 
 
CFM-ID 4.0 ' a web server for accurate MS-based metabolite identification border= 
 
Fei Wang; Dana Allen; Siyang Tian; Eponine Oler ; Vasuk Gautam ...
 
 
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data border= 
 
Zhaonan Zou; Tazro Ohta; Fumihito Miura ; Shinya Oki
 
 
CircadiOmics: circadian omic web portal border= 
 
Muntaha Samad; Forest Agostinelli; Tomoki Sato; Kohei Shimaji ; Pierre Baldi
 
 
CRISPRedict: a CRISPR-Cas9 web tool for interpretable efficiency predictions border= 
 
Vasileios Konstantakos; Anastasios Nentidis; Anastasia Krithara; Georgios Paliouras
 
 
Identification of genome edited cells using CRISPRnano border= 
 
Thach Nguyen; Haribaskar Ramachandran; Soraia Martins; Jean Krutmann ; Andrea Rossi
 
 
CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning border= 
 
Carlos H M Rodrigues; David B Ascher
 
 
Dali server: structural unification of protein families border= 
 
Liisa Holm
 
 
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update) 
 
Brad T Sherman; Ming Hao; Ju Qiu; Xiaoli Jiao ; Michael W Baseler ...
 
 
DDGun: an untrained predictor of protein stability changes upon amino acid variants border= 
 
Ludovica Montanucci; Emidio Capriotti; Giovanni Birolo ; Silvia Benevenuta; Corrado Pancotti ...
 
 
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models border= 
 
Vineet Thumuluri; José Juan Almagro Armenteros; Alexander Rosenberg Johansen ; Henrik Nielsen; Ole Winther
 
 
DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction border= 
 
Xiaogen Zhou; Chunxiang Peng; Wei Zheng ; Yang Li; Guijun Zhang ...
 
 
DEPCOD: a tool to detect and visualize co-evolution of protein domains border= 
 
Fei Ji; Gracia Bonilla; Rustem Krykbaev; Gary Ruvkun ; Yuval Tabach ...
 
 
DLEB: a web application for building deep learning models in biological research border= 
 
Suyeon Wy; Daehong Kwon; Kisang Kwon; Jaebum Kim
 
 
DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes border= 
 
Razieh Mohammadi-Arani; Fatemeh Javadi-Zarnaghi; Pietro Boccaletto ; Janusz M Bujnicki; Almudena Ponce-Salvatierra
 
 
Web-based platform for analysis of RNA folding from high throughput chemical probing data border= 
 
Christopher P Jurich; Amir Brivanlou; Silvi Rouskin ; Joseph D Yesselman
 
 
DrugVirus.info 2.0: an integrative data portal for broad-spectrum antivirals (BSA) and BSA-containing drug combinations (BCCs) border= 
 
Aleksandr Ianevski; Ronja M Simonsen; Vegard Myhre ; Tanel Tenson; Valentyn Oksenych ...
 
 
Search and sequence analysis tools services from EMBL-EBI in 2022 border= 
 
Fábio Madeira; Matt Pearce; Adrian R N Tivey; Prasad Basutkar ; Joon Lee ...
 
 
enrichMiR predicts functionally relevant microRNAs based on target collections border= 
 
Michael Soutschek; Tomás Germade; Pierre-Luc Germain ; Gerhard Schratt
 
 
EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions border= 
 
Li Tang; Zhizhou Zhong; Yisheng Lin ; Yifei Yang; Jun Wang ...
 
 
ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database border= 
 
Zhitao Mao; Ruoyu Wang; Haoran Li ; Yixin Huang; Qiang Zhang ...
 
 
ExPheWas: a platform for cis-Mendelian randomization and gene-based association scans border= 
 
Marc-André Legault; Louis-Philippe Lemieux Perreault; Jean-Claude Tardif ; Marie-Pierre Dubé
 
 
ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data border= 
 
Xian Liu; Kaikun Xu; Xin Tao; Ronghua Yin; Guangming Ren ...
 
 
FABIAN-variant: predicting the effects of DNA variants on transcription factor binding border= 
 
Robin Steinhaus; Peter N Robinson; Dominik Seelow
 
 
FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes border= 
 
Anne de Jong; Oscar P Kuipers; Jan Kok
 
 
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid'liquid phase separation and aggregation of proteins border= 
 
Andras Hatos; Silvio C E Tosatto; Michele Vendruscolo ; Monika Fuxreiter
 
 
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update border= 
 
Enis Afgan; Anton Nekrutenko; Bjórn A Grüning ; Daniel Blankenberg; Jeremy Goecks ...
 
 
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective border= 
 
Jorge Botas; Álvaro Rodríguez del Río; Joaquín Giner-Lamia ; Jaime Huerta-Cepas
 
 
GenePlexus: a web-server for gene discovery using network-based machine learning border= 
 
Christopher A Mancuso; Patrick S Bills; Douglas Krum; Jacob Newsted ; Renming Liu ...
 
 
GEOexplorer: a webserver for gene expression analysis and visualisation border= 
 
Guy P Hunt; Luigi Grassi; Rafael Henkin; Fabrizio Smeraldi ; Thomas P Spargo ...
 
 
GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA border= 
 
Nur Syatila Ab Ghani; Reeki Emrizal; Sabrina Mohamed Moffit ; Hazrina Yusof Hamdani; Effirul Ikhwan Ramlan ...
 
 
GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents border= 
 
Erich R Kuechler; Matthew Jacobson; Thibault Mayor ; Jörg Gsponer
 
 
GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs border= 
 
Charles A Santana; Sandro C Izidoro; Raquel C de Melo-Minardi ; Jonathan D Tyzack; António J M Ribeiro ...
 
 
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods border= 
 
Deniz SeçilmiÅŸ; Thomas Hillerton; Erik L L Sonnhammer
 
 
HemI 2.0: an online service for heatmap illustration border= 
 
Wanshan Ning; Yuxiang Wei; Letian Gao; Cheng Han ; Yujie Gou ...
 
 
iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families border= 
 
Francesco Oteri; Edoardo Sarti; Francesca Nadalin ; Alessandra Carbone
 
 
IBS 2.0: an upgraded illustrator for the visualization of biological sequences border= 
 
Yubin Xie; Huiqin Li; Xiaotong Luo; Hongyu Li ; Qiuyuan Gao ...
 
 
ICARUS, an interactive web server for single cell RNA-seq analysis border= 
 
Andrew Jiang; Klaus Lehnert; Linya You; Russell G Snell
 
 
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets border= 
 
Zhen Chen; Xuhan Liu; Pei Zhao ; Chen Li; Yanan Wang ...
 
 
KmerKeys: a web resource for searching indexed genome assemblies and variants border= 
 
Dmitri S Pavlichin; HoJoon Lee; Stephanie U Greer; Susan M Grimes ; Tsachy Weissman ...
 
 
LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation border= 
 
Wei Zheng; Qiqige Wuyun; Xiaogen Zhou ; Yang Li; Peter L Freddolino ...
 
 
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering border= 
 
Joan Planas-Iglesias; Filip Opaleny; Pavol Ulbrich ; Jan Stourac; Zainab Sanusi ...
 
 
MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes border= 
 
Aleksandra E Badaczewska-Dawid; Chandran Nithin; Karol Wroblewski ; Mateusz Kurcinski; Sebastian Kmiecik
 
 
MDsrv: visual sharing and analysis of molecular dynamics simulations border= 
 
Michelle Kampfrath; René Staritzbichler; Guillermo Pérez Hernández; Alexander S Rose ; Johanna K S Tiemann ...
 
 
The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context border= 
 
Fabio Marchiano; Margaux Haering; Bianca Hermine Habermann
 
 
Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes border= 
 
Shu-Cheng Liu; Yan-Ru Ju; Chin Lung Lu
 
 
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning border= 
 
Magnus Haraldson Høie; Erik Nicolas Kiehl; Bent Petersen ; Morten Nielsen; Ole Winther ...
 
 
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes border= 
 
Caroline Vernette; Julien Lecubin; Pablo Sánchez ; Silvia G Acinas; Marcel Babin ...
 
 
OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics border= 
 
Guangyan Zhou; Zhiqiang Pang; Yao Lu ; Jessica Ewald; Jianguo Xia
 
 
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins border= 
 
Ivan S Ilnitskiy; Anastasia A Zharikova; Andrey A Mironov
 
 
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes border= 
 
Leighton J Payne; Sean Meaden; Mario R Mestre ; Chris Palmer; Nicolás Toro ...
 
 
PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases border= 
 
Tianyuan Liu; Pedro Salguero; Marko Petek ; Carlos Martinez-Mira; Leandro Balzano-Nogueira ...
 
 
patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures border= 
 
Mirko Schmitz; Anne Schultze; Raimonds Vanags ; Karsten Voigt; Barbara Di Ventura ...
 
 
PCGA: a comprehensive web server for phenotype-cell-gene association analysis border= 
 
Chao Xue; Lin Jiang; Miao Zhou; Qihan Long ; Ying Chen ...
 
 
PhyloCloud: an online platform for making sense of phylogenomic data border= 
 
Ziqi Deng; Jorge Botas; Carlos P Cantalapiedra; Ana Hernández-Plaza ; Jordi Burguet-Castell ...
 
 
PiER: web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions border= 
 
Hai Fang
 
 
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures border= 
 
David Jakubec; Petr Skoda; Radoslav Krivak ; Marian Novotny; David Hoksza
 
 
PRECOGx: exploring GPCR signaling mechanisms with deep protein representations border= 
 
Marin Matic; Gurdeep Singh; Francesco Carli ; Natalia De Oliveira Rosa; Pasquale Miglionico ...
 
 
ProteinsPlus: a comprehensive collection of web-based molecular modeling tools border= 
 
Katrin Schöning-Stierand; Konrad Diedrich; Christiane Ehrt ; Florian Flachsenberg; Joel Graef ...
 
 
pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature border= 
 
Peng-Hsuan Li; Ting-Fu Chen; Jheng-Ying Yu ; Shang-Hung Shih; Chan-Hung Su ...
 
 
The Quest for Orthologs orthology benchmark service in 2022 border= 
 
Yannis Nevers; Tamsin E M Jones; Dushyanth Jyothi; Bethan Yates ; Meritxell Ferret ...
 
 
RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets border= 
 
Lei Zheng; Dongyang Liu; Yuan Alex Li ; Siqi Yang; Yuchao Liang ...
 
 
REVERSE: a user-friendly web server for analyzing next-generation sequencing data from in vitro selection/evolution experiments border= 
 
Zoe Weiss; Saurja DasGupta
 
 
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles border= 
 
Damiano Clementel; Alessio Del Conte; Alexander Miguel Monzon ; Giorgia F Camagni; Giovanni Minervini ...
 
 
rna-tools.online: a Swiss army knife for RNA 3D structure modeling workflow border= 
 
Marcin Magnus
 
 
RNAspider: a webserver to analyze entanglements in RNA 3D structures border= 
 
Kamil Luwanski; Vladyslav Hlushchenko; Mariusz Popenda; Tomasz Zok ; Joanna Sarzynska ...
 
 
RSAT 2022: regulatory sequence analysis tools border= 
 
Walter Santana-Garcia; Jaime A Castro-Mondragon; Mónica Padilla-Gálvez; Nga Thi Thuy Nguyen ; Ana Elizondo-Salas ...
 
 
Deep phenotyping: symptom annotation made simple with SAMS border= 
 
Robin Steinhaus; Sebastian Proft; Evelyn Seelow; Tobias Schalau ; Peter N Robinson ...
 
 
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria border= 
 
Mehmet Direnç Mungan; Theresa Anisja Harbig; Naybel Hernandez Perez ; Simone Edenhart; Evi Stegmann ...
 
 
Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks border= 
 
Mariia Emelianova; Anastasiia Gainullina; Nikolay Poperechnyi ; Alexander Loboda; Maxim Artyomov ...
 
 
SigCom LINCS: data and metadata search engine for a million gene expression signatures border= 
 
John Erol Evangelista; Daniel J B Clarke; Zhuorui Xie ; Alexander Lachmann; Minji Jeon ...
 
 
sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms border= 
 
Ernesto Aparicio-Puerta; Cristina Gómez-Martín; Stavros Giannoukakos ; José María Medina; Chantal Scheepbouwer ...
 
 
SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment border= 
 
Joanne Watson; Michael Smith; Chiara Francavilla ; Jean-Marc Schwartz
 
 
SuperPred 3.0: drug classification and target prediction'a machine learning approach border= 
 
Kathleen Gallo; Andrean Goede; Robert Preissner ; Bjoern-Oliver Gohlke
 
 
SWORD2: hierarchical analysis of protein 3D structures border= 
 
Gabriel Cretin; Tatiana Galochkina; Yann Vander Meersche; Alexandre G de Brevern ; Guillaume Postic ...
 
 
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples border= 
 
Aleksandr Ianevski; Anil K Giri; Tero Aittokallio
 
 
TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure border= 
 
Barbara Poszewiecka; Victor Murcia Pienkowski; Karol Nowosad ; Jérôme D Robin; Krzysztof Gogolewski ...
 
 
TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research border= 
 
Dominique Sydow; Jaime Rodríguez-Guerra; Talia B Kimber ; David Schaller; Corey J Taylor ...
 
 
TIRSF: a web server for screening gene signatures to predict Tumor immunotherapy response border= 
 
Li Chen; Tianjian Chen; Ya Zhang ; Haichen Lin; Ruihan Wang ...
 
 
VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens border= 
 
Meng Wang; Ying-Xian Goh; Cui Tai ; Hui Wang; Zixin Deng ...
 
 
WashU Epigenome Browser update 2022 border= 
 
Daofeng Li; Deepak Purushotham; Jessica K Harrison; Silas Hsu ; Xiaoyu Zhuo ...
 
 
WebCSEA: web-based cell-type-specific enrichment analysis of genes border= 
 
Yulin Dai; Ruifeng Hu; Andi Liu; Kyung Serk Cho ; Astrid Marilyn Manuel ...
 
 
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