Subject: Nucleic Acids Research Table of Contents for 5 July 2024 Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Celebrating 50 years of NAR
 

Nucleic Acids Research is celebrating its 50th anniversary this year. We owe our success to the incredible work of the three founding editors, Richard T. Walker and A. Stanley Jones at the University of Birmingham in the UK, and Dieter Söll at Yale University in the USA. Their vision and dedication have been carried forward by the editors who followed them, as well as our authors and reviewers. Today, NAR remains one of the leading journals in the biological sciences. 

Celebrate our 50th anniversary with us
 
 
 
 
Nucleic Acids Research  
Volume 52 Issue W1
 
5 July 2024
 
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EDITORIAL
 
 
 
 
The 22nd annual Nucleic Acids Research Web Server Issue 2024 border= 
 
Dominik Seelow
 
 
 
DNA
 
 
 
 
Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers border=  
 
Jinsen Li, Remo Rohs
 
 
 
DNAforge: a design tool for nucleic acid wireframe nanostructures border=  
 
Antti Elonen, Leon Wimbes, Abdulmelik Mohammed, Pekka Orponen
 
 
 
iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning border= 
 
Haopeng Yu, Fan Li, Bibo Yang, Yiman Qi, Dilek Guneri ...
 
 
 
EVOLUTION, GENETICS, GENOMICS, GENOME EDITING
 
 
 
 
AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach border= 
 
Serena Rosignoli, Elisa Lustrino, Alessio Conci, Alessandra Fabrizi, Serena Rinaldo ...
 
 
 
 
Annotation and visualization of parasite, fungi and arthropod genomes with Companion border= 
 
William Haese-Hill, Kathryn Crouch, Thomas D Otto
 
 
 
ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data border= 
 
Zhaonan Zou, Tazro Ohta, Shinya Oki
 
 
 
DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data border= 
 
Keith D Harris, Gili Greenbaum
 
 
 
Drawing human pedigree charts with DrawPed border=  
 
Janina Schönberger, Robin Steinhaus, Dominik Seelow
 
 
 
FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes border= 
 
Jérôme Montfort, Francisca Hervas-Sotomayor, Aurélie Le Cam, Florent Murat
 
 
 
 
Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers border= 
 
Lukas Forer, Daniel Taliun, Jonathon LeFaive, Albert V Smith, Andrew P Boughton ...
 
 
 
Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool border= 
 
Ivica Letunic, Peer Bork
 
 
 
The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update border= 
 
Linelle Ann L Abueg, Enis Afgan, Olivier Allart, Ahmed H Awan, Wendi A Bacon ...
 
 
 
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs border= 
 
Shikuan Zhang, Songmao Wang, Fang Lu, Lingzi Bie, Yongjiang Luo ...
 
 
 
mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics border= 
 
Hansi Weissensteiner, Lukas Forer, Florian Kronenberg, Sebastian Schönherr
 
 
 
NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data border= 
 
Bogdan Efimenko, Konstantin Popadin, Konstantin Gunbin
 
 
 
SeqCAT: Sequence Conversion and Analysis Toolbox border=  
 
Kevin Kornrumpf, Nadine S Kurz, Klara Drofenik, Lukas Krauß, Carolin Schneider ...
 
 
 
SynDesign: web-based prime editing guide RNA design and evaluation tool for saturation genome editing border= 
 
Jinman Park, Goosang Yu, Sang-Yeon Seo, Jinyeong Yang, Hyongbum Henry Kim
 
 
 
TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms border= 
 
Yuzhuo Li, Renzhe Lyu, Shuai Chen, Yejun Wang, Ming-an Sun
 
 
 
VARIANT ASSESSMENT
 
 
 
 
MutationExplorer : a webserver for mutation of proteins and 3D visualization of energetic impacts border= 
 
Michelle Philipp, Christopher W Moth, Nikola Ristic, Johanna K S Tiemann, Florian Seufert ...
 
 
 
ProtVar: mapping and contextualizing human missense variation border=  
 
James D Stephenson, Prabhat Totoo, David F Burke, Jürgen Jänes, Pedro Beltrao ...
 
 
 
REEV: review, evaluate and explain variants border=  
 
Dzmitry Hramyka, Henrike Lisa Sczakiel, Max Xiaohang Zhao, Oliver Stolpe, Mikko Nieminen ...
 
 
 
PROTEINS
 
 
 
 
AggreProt: a web server for predicting and engineering aggregation prone regions in proteins border= 
 
Joan Planas-Iglesias, Simeon Borko, Jan Swiatkowski, Matej Elias, Martin Havlasek ...
 
 
 
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation border=  
 
Oriol Bárcenas, Aleksander Kuriata, Mateusz Zalewski, Valentín Iglesias, Carlos Pintado-Grima ...
 
 
 
AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder border= 
 
Gábor ErdÅ's, Zsuzsanna Dosztányi
 
 
 
AlphaFind: discover structure similarity across the proteome in AlphaFold DB border=  
 
David Procházka, Terézia Slanináková, Jaroslav Olha, Adrián RoÅ¡inec, Katarína GreÅ¡ová ...
 
 
 
AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models border= 
 
Pawel Rubach, Maciej Sikora, Aleksandra I Jarmolinska, Agata P Perlinska, Joanna I Sulkowska
 
 
 
CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds border= 
 
Bowei Ye, Wei Tian, Boshen Wang, Jie Liang
 
 
 
The Damietta Server: a comprehensive protein design toolkit border=  
 
Iwan Grin, Kateryna Maksymenko, Tobias Wörtwein, Mohammad ElGamacy
 
 
 
DDMut-PPI: predicting effects of mutations on protein'protein interactions using graph-based deep learning border= 
 
Yunzhuo Zhou, YooChan Myung, Carlos H M Rodrigues, David B Ascher
 
 
 
DeepLoc 2.1: multi-label membrane protein type prediction using protein language models border= 
 
Marius Thrane Ødum, Felix Teufel, Vineet Thumuluri, José Juan Almagro Armenteros, Alexander Rosenberg Johansen ...
 
 
 
DEGRONOPEDIA: a web server for proteome-wide inspection of degrons border=  
 
Natalia A Szulc, Filip Stefaniak, MaÅ‚gorzata Piechota, Anna SoszyÅ"ska, Gabriela Piórkowska ...
 
 
 
Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families border= 
 
R Gonzalo Parra, Maria I Freiberger, Miriam Poley-Gil, Miguel Fernandez-Martin, Leandro G Radusky ...
 
 
 
GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs border= 
 
Yujie Gou, Dan Liu, Miaomiao Chen, Yuxiang Wei, Xinhe Huang ...
 
 
 
GPSFun: geometry-aware protein sequence function predictions with language models border= 
 
Qianmu Yuan, Chong Tian, Yidong Song, Peihua Ou, Mingming Zhu ...
 
 
 
MinActionPath2: path generation between different conformations of large macromolecular assemblies by action minimization border= 
 
Patrice Koehl, Rafael Navaza, Mustafa Tekpinar, Marc Delarue
 
 
 
PPI3D: a web server for searching, analyzing and modeling protein'protein, protein'peptide and protein'nucleic acid interactions border= 
 
Justas DapkÅ«nas, Albertas Timinskas, Kliment OlechnoviÄ, MiglÄ- TomkuvienÄ-, Ä'eslovas Venclovas
 
 
 
PROSCA: an online platform for humanized scaffold mining facilitating rational protein engineering border= 
 
Xiaona Wang, Yintao Zhang, Zengpeng Li, Zixin Duan, Menghan Guo ...
 
 
 
Proscan: a structure-based proline design web server border=  
 
Nathaniel Felbinger, Helder V Ribeiro-Filho, Brian G Pierce
 
 
 
Deep learning for the PSIPRED Protein Analysis Workbench border=  
 
Daniel W A Buchan, Lewis Moffat, Andy Lau, Shaun M Kandathil, David T Jones
 
 
 
PypKa server: online pKa predictions and biomolecular structure preparation with precomputed data from PDB and AlphaFold DB border= 
 
Pedro B P S Reis, Djork-Arné Clevert, Miguel Machuqueiro
 
 
 
REME: an integrated platform for reaction enzyme mining and evaluation border=  
 
Zhenkun Shi, Dehang Wang, Yang Li, Rui Deng, Jiawei Lin ...
 
 
 
RING 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures border= 
 
Alessio Del Conte, Giorgia F Camagni, Damiano Clementel, Giovanni Minervini, Alexander Miguel Monzon ...
 
 
 
SLiMAn 2.0: meaningful navigation through peptide-protein interaction networks border= 
 
Victor Reys, Jean-Luc Pons, Gilles Labesse
 
 
 
The structure assessment web server: for proteins, complexes and more border=  
 
Andrew M Waterhouse, Gabriel Studer, Xavier Robin, Stefan Bienert, Gerardo Tauriello ...
 
 
 
SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina border= 
 
Marine Bugnon, Ute F Röhrig, Mathilde Goullieux, Marta A S Perez, Antoine Daina ...
 
 
 
WeSA: a web server for improving analysis of affinity proteomics data border=  
 
Magdalena M Shtetinska, Juan-Carlos González-Sánchez, Tina Beyer, Karsten Boldt, Marius Ueffing ...
 
 
 
RNA
 
 
 
 
IsoVis ' a webserver for visualization and annotation of alternative RNA isoforms border= 
 
Ching Yin Wan, Jack Davis, Manveer Chauhan, Josie Gleeson, Yair D J Prawer ...
 
 
 
RNAhugs web server for customized 3D RNA structure alignment border=  
 
Michal Zurkowski, Mateusz Swiercz, Filip Wozny, Maciej Antczak, Marta Szachniuk
 
 
 
RNAscape: geometric mapping and customizable visualization of RNA structure border=  
 
Raktim Mitra, Ari S Cohen, Remo Rohs
 
 
 
SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data border= 
 
Niek R Scholten, Dennis Haandrikman, Joshua O Tolhuis, Edoardo Morandi, Danny Incarnato
 
 
 
SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories border= 
 
S Naeim Moafinejad, Belisa R H de Aquino, MichaÅ‚ J Boniecki, Iswarya P N Pandaranadar Jeyeram, Grigory Nikolaev ...
 
 
 
SingmiR: a single-cell miRNA alignment and analysis tool border=  
 
Annika Engel, Shusruto Rishik, Pascal Hirsch, Verena Keller, Tobias Fehlmann ...
 
 
 
METABOLOMICS, LIPIDOMICS, MICROBIOME
 
 
 
 
GCMS-ID: a webserver for identifying compounds from gas chromatography mass spectrometry experiments border= 
 
Julia Wakoli, Afia Anjum, Tanvir Sajed, Eponine Oler, Fei Wang ...
 
 
 
LipidSig 2.0: integrating lipid characteristic insights into advanced lipidomics data analysis border= 
 
Chia-Hsin Liu, Pei-Chun Shen, Wen-Jen Lin, Hsiu-Cheng Liu, Meng-Hsin Tsai ...
 
 
 
MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation border= 
 
Zhiqiang Pang, Yao Lu, Guangyan Zhou, Fiona Hui, Lei Xu ...
 
 
 
Mibianto: ultra-efficient online microbiome analysis through k -mer based metagenomics border= 
 
Pascal Hirsch, Leidy-Alejandra G Molano, Annika Engel, Jens Zentgraf, Sven Rahmann ...
 
 
 
WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics border= 
 
John M Elizarraras, Yuxing Liao, Zhiao Shi, Qian Zhu, Alexander R Pico ...
 
 
 
CHEMINFORMATICS, PHARMACOKINETICS
 
 
 
 
ADMETlab 3.0: an updated comprehensive online ADMET prediction platform enhanced with broader coverage, improved performance, API functionality and decision support border= 
 
Li Fu, Shaohua Shi, Jiacai Yi, Ningning Wang, Yuanhang He ...
 
 
 
admetSAR3.0: a comprehensive platform for exploration, prediction and optimization of chemical ADMET properties border= 
 
Yaxin Gu, Zhuohang Yu, Yimeng Wang, Long Chen, Chaofeng Lou ...
 
 
 
ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery border= 
 
Shaohua Shi, Li Fu, Jiacai Yi, Ziyi Yang, Xiaochen Zhang ...
 
 
 
ChemFREE: a one-stop comprehensive platform for ecological and environmental risk evaluation of chemicals in one health world border= 
 
Dongyu Chen, Yingwei Liu, Yang Liu, Kejun Zhao, Tianhan Zhang ...
 
 
 
ChemoDOTS: a web server to design chemistry-driven focused libraries border=  
 
Laurent Hoffer, Guillaume Charifi-Hoareau, Sarah Barelier, Stéphane Betzi, Thomas Miller ...
 
 
 
Deep-PK: deep learning for small molecule pharmacokinetic and toxicity prediction border= 
 
Yoochan Myung, Alex G C de Sá, David B Ascher
 
 
 
DetSpace: a web server for engineering detectable pathways for bio-based chemical production border= 
 
Hèctor Martín Lázaro, Ricardo Marín Bautista, Pablo Carbonell
 
 
 
Drugst.One ' a plug-and-play solution for online systems medicine and network-based drug repurposing border= 
 
Andreas Maier, Michael Hartung, Mark Abovsky, Klaudia Adamowicz, Gary D Bader ...
 
 
 
KinomeMETA: a web platform for kinome-wide polypharmacology profiling with meta-learning border= 
 
Zhaojun Li, Ning Qu, Jingyi Zhou, Jingjing Sun, Qun Ren ...
 
 
 
MolModa: accessible and secure molecular docking in a web browser border=  
 
Yuri Kochnev, Mayar Ahmed, Alex M Maldonado, Jacob D Durrant
 
 
 
Pred-O3, a web server to predict molecules, olfactory receptors and odor relationships border= 
 
Guillaume Ollitrault, Rayane Achebouche, Antoine Dreux, Samuel Murail, Karine Audouze ...
 
 
 
ProTox 3.0: a webserver for the prediction of toxicity of chemicals border=  
 
Priyanka Banerjee, Emanuel Kemmler, Mathias Dunkel, Robert Preissner
 
 
 
OTHERS
 
 
 
 
The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 border= 
 
Fábio Madeira, Nandana Madhusoodanan, Joonheung Lee, Alberto Eusebi, Ania Niewielska ...
 
 
 
Next-generation IEDB tools: a platform for epitope prediction and analysis border=  
 
Zhen Yan, Kevin Kim, Haeuk Kim, Brendan Ha, Anaïs Gambiez ...
 
 
 
SEMA 2.0: web-platform for B-cell conformational epitopes prediction using artificial intelligence border= 
 
Nikita V Ivanisenko, Tatiana I Shashkova, Andrey Shevtsov, Maria Sindeeva, Dmitriy Umerenkov ...
 
 
 
PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge 
 
Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian ...
 
 
 
TTSBBC: triplex target site biomarkers and barcodes in cancer border=  
 
Maya Ylagan, Qi Xu, Jeanne Kowalski
 
 
 
CORRECTIONS
 
 
 
 
Correction to ˜SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories' border= 
 
 
 
 
Correction to ˜ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery' border= 
 
 
 
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