Nucleic acids research

Keyphrases

Publications

volume 52, number W1, 2024

Yujie Gou, Dan Liu, Miaomiao Chen, Yuxiang Wei, Xinhe Huang, Cheng Han, Zihao Feng, Chi Zhang, Teng Lu, Di Peng, Yang Xu
GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs. Nucleic acids research 52 (W1) (2024)
Hèctor Martín Lázaro, Ricardo Marín Bautista, Pablo Carbonell
DetSpace: a web server for engineering detectable pathways for bio-based chemical production. Nucleic acids research 52 (W1) (2024)
Michelle Kampfrath, Christopher W Moth, Nikola Ristic, Johanna K S Tiemann, Florian Seufert, Aleksandra Panfilova, Jens Meiler, Peter W Hildebrand, Amelie Stein, Daniel Wiegreffe, René Staritzbichler
MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts. Nucleic acids research 52 (W1) (2024)
Oriol Bárcenas, Aleksander Kuriata, Mateusz Zalewski, Valentin Iglesias, Carlos Pintado, Grzegorz Firlik, Burdukiewicz Michał, Sebastian Kmiecik, Salvador Ventura
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation. Nucleic acids research 52 (W1) (2024)
Jerome Montfort, Francisca Hervas-Sotomayor, Aurélie Le Cam, Florent Murat
FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes. Nucleic acids research 52 (W1) (2024)
Hansi Weissensteiner, Lukas Forer, Florian Kronenberg, Sebastian Schönherr
mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics. Nucleic acids research 52 (W1) (2024)
Maya Ylagan, Qi Xu, Jeanne Kowalski
TTSBBC: triplex target site biomarkers and barcodes in cancer. Nucleic acids research 52 (W1) (2024)
Iwan Grin, Kateryna Maksymenko, Tobias Wörtwein, Mohammad ElGamacy
The Damietta Server: a comprehensive protein design toolkit. Nucleic acids research 52 (W1) (2024)
Ivica Letunic, Peer Bork
Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic acids research 52 (W1) (2024)
Fábio Madeira, Nandana Madhusoodanan, Joonheung Lee, Alberto Eusebi, Ania Niewielska, Adrian R N Tivey, Rodrigo Lopez, Sarah A Butcher
The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024. Nucleic acids research 52 (W1) (2024)
Xiaona Wang, Yintao Zhang, Zengpeng Li, Zixin Duan, Menghan Guo, Zhen Wang, Jian Zhang, Wei Wei Xue
PROSCA: an online platform for humanized scaffold mining facilitating rational protein engineering. Nucleic acids research 52 (W1) (2024)
Li Fu, Shao-Hua Shi, Jia-Cai Yi, Ningning Wang, Yuanhang He, Zhenxing Wu, Jinfu Peng, Youchao Deng, Wenxuan Wang, Chengkun Wu, Ai-Ping Lu, Xiangxiang Zeng, Wentao Zhao, Ting-Jun Hou, Dong-Sheng Cao
ADMETlab 3.0: an updated comprehensive online ADMET prediction platform enhanced with broader coverage, improved performance, API functionality and decision support. Nucleic acids research 52 (W1) (2024)
Shikuan Zhang, Songmao Wang, Fang Lu, Lingzi Bie, Yongjiang Luo, Jiahe Sun, Yang Zhang, Yi Wang, Yaou Zhang, Qing Rex Lyu
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs. Nucleic acids research 52 (W1) (2024)
Chia-Hsin Liu, Pei-Chun Shen, Wen-Jen Lin, Hsiu-Cheng Liu, Meng-Hsin Tsai, Tzu-Ya Huang, I-Chieh Chen, Yo-Liang Lai, Yu-De Wang, Mien-Chie Hung, Wei-Chung Cheng
LipidSig 2.0: integrating lipid characteristic insights into advanced lipidomics data analysis. Nucleic acids research 52 (W1) (2024)
Keith D Harris, Gili Greenbaum
DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data. Nucleic acids research 52 (W1) (2024)
Marine Bugnon, Ute F Röhrig, Mathilde Goullieux, Marta A S Perez, Antoine Daina, Olivier Michielin, Vincent Zoete
SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic acids research 52 (W1) (2024)
Jinman Park, Goosang Yu, Sang-Yeon Seo, Jinyeong Yang, Hyongbum Henry Kim
SynDesign: web-based prime editing guide RNA design and evaluation tool for saturation genome editing. Nucleic acids research 52 (W1) (2024)
Priyanka Banerjee, Emanuel Kemmler, Mathias Dunkel, Filippo De Braud
ProTox 3.0: a webserver for the prediction of toxicity of chemicals. Nucleic acids research 52 (W1) (2024)
Niek R Scholten, Dennis Haandrikman, Joshua O Tolhuis, Edoardo Morandi, Danny Incarnato
SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data. Nucleic acids research 52 (W1) (2024)
Pedro B P S Reis, Djork-Arné Clevert, Miguel Machuqueiro
PypKa server: online pKa predictions and biomolecular structure preparation with precomputed data from PDB and AlphaFold DB. Nucleic acids research 52 (W1) (2024)
Andrew M Waterhouse, Gabriel Studer, Xavier Robin, Stefan Bienert, Gerardo Tauriello, Torsten Schwede
The structure assessment web server: for proteins, complexes and more. Nucleic acids research 52 (W1) (2024)
Michal Zurkowski, Mateusz Swiercz, Filip Wozny, Maciej Antczak, Marta Szachniuk
RNAhugs web server for customized 3D RNA structure alignment. Nucleic acids research 52 (W1) (2024)
Yuzhuo Li, Renzhe Lyu, Shuai Chen, Yejun Wang, Ming-An Sun
TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms. Nucleic acids research 52 (W1) (2024)
Marius Thrane Ødum, Felix Teufel, Vineet Thumuluri, José Juan Almagro Armenteros, Alexander Rosenberg Johansen, Ole Winther, Henrik Nielsen
DeepLoc 2.1: multi-label membrane protein type prediction using protein language models. Nucleic acids research 52 (W1) (2024)
R Gonzalo Parra, Maria I Freiberger, Miriam Poley-Gil, Miguel Fernandez-Martin, Leandro G Radusky, Victoria Ruiz-Serra, Peter G Wolynes, Diego U Ferreiro, Alfonso Valencia
Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families. Nucleic acids research 52 (W1) (2024)
Qianmu Yuan, Chong Tian, Yidong Song, Peihua Ou, Mingming Zhu, Huiying Zhao, Yuedong Yang
GPSFun: geometry-aware protein sequence function predictions with language models. Nucleic acids research 52 (W1) (2024)
Annika Engel, Shusruto Rishik, Pascal Hirsch, Verena Keller, Tobias Fehlmann, Fabian Kern, Andreas Keller
SingmiR: a single-cell miRNA alignment and analysis tool. Nucleic acids research 52 (W1) (2024)
S Naeim Moafinejad, Belisa R H de Aquino, Michał J Boniecki, Iswarya P N Pandaranadar Jeyeram, Grigory Nikolaev, Marcin Magnus, Masoud Amiri Farsani, Nagendar Goud Badepally, Tomasz K Wirecki, Filip Stefaniak, Janusz M Bujnicki
SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories. Nucleic acids research 52 (W1) (2024)
Janina Schönberger, Robin Steinhaus, Dominik Seelow
Drawing human pedigree charts with DrawPed. Nucleic acids research 52 (W1) (2024)
Gábor Erdős, Zsuzsanna Dosztányi
AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder. Nucleic acids research 52 (W1) (2024)
Pascal Hirsch, Leidy-Alejandra G Molano, Annika Engel, Jens Zentgraf, Sven Rahmann, Matthias Hannig, Rolf Müller, Fabian Kern, Andreas Keller, Georges P Schmartz
Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics. Nucleic acids research 52 (W1) (2024)
Nikita V Ivanisenko, Tatiana I Shashkova, Andrey Shevtsov, Maria Sindeeva, Dmitriy Umerenkov, Olga Kardymon
SEMA 2.0: web-platform for B-cell conformational epitopes prediction using artificial intelligence. Nucleic acids research 52 (W1) (2024)
Lukas Forer, Daniel Taliun, Jonathon LeFaive, Albert V Smith, Andrew P Boughton, Stefan Coassin, Claudia Lamina, Florian Kronenberg, Christian Fuchsberger, Sebastian Schönherr
Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers. Nucleic acids research 52 (W1) (2024)
David Procházka, Terézia Slanináková, Jaroslav Olha, Adrián Rošinec, Katarína Grešová, Miriama Jánošová, Jakub Čillík, Jana Porubská, Radka Svobodová, Vlastislav Dohnal, Matej Antol
AlphaFind: discover structure similarity across the proteome in AlphaFold DB. Nucleic acids research 52 (W1) (2024)
Laurent Hoffer, Guillaume Charifi-Hoareau, Sarah Barelier, Stéphane Betzi, Thomas W Miller, Xavier Morelli, Philippe Roche
ChemoDOTS: a web server to design chemistry-driven focused libraries. Nucleic acids research 52 (W1) (2024)
Alessio Del Conte, Giorgia F Camagni, Damiano Clementel, Giovanni Minervini, Alexander Miguel Monzon, Carlo Ferrari, Damiano Piovesan, Silvio C E Tosatto
RING 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures. Nucleic acids research 52 (W1) (2024)
Haopeng Yu, Fan Li, Bibo Yang, Yiman Qi, Dilek Guneri, Wenqian Chen, Zoë A E Waller, Ke Li, Yiliang Ding
iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning. Nucleic acids research 52 (W1) (2024)
Ching Yin Wan, Jack Davis, Manveer Chauhan, Josie Gleeson, Yair D J Prawer, Ricardo De Paoli-Iseppi, Christine A Wells, Jarny Choi, Michael B Clark
IsoVis - a webserver for visualization and annotation of alternative RNA isoforms. Nucleic acids research 52 (W1) (2024)
Yaxin Gu, Zhuohang Yu, Yimeng Wang, Long Chen, Chaofeng Lou, Chen Yang, Weihua Li, Guixia Liu, Yun Tang
admetSAR3.0: a comprehensive platform for exploration, prediction and optimization of chemical ADMET properties. Nucleic acids research 52 (W1) (2024)
Guillaume Ollitrault, Rayane Achebouche, Antoine Dreux, Samuel Murail, Karine Audouze, Anne Tromelin, Olivier Taboureau
Pred-O3, a web server to predict molecules, olfactory receptors and odor relationships. Nucleic acids research 52 (W1) (2024)
Yoochan Myung, Alex G C de Sá, David Benjamin Ascher
Deep-PK: deep learning for small molecule pharmacokinetic and toxicity prediction. Nucleic acids research 52 (W1) (2024)
Zhaonan Zou, Tazro Ohta, Shinya Oki
ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data. Nucleic acids research 52 (W1) (2024)
Justas Dapkunas, Albertas Timinskas, Kliment Olechnovič, Miglė Tomkuvienė, Česlovas Venclovas
PPI3D: a web server for searching, analyzing and modeling protein-protein, protein-peptide and protein-nucleic acid interactions. Nucleic acids research 52 (W1) (2024)
Raktim Mitra, Ari S Cohen, Remo Rohs
RNAscape: geometric mapping and customizable visualization of RNA structure. Nucleic acids research 52 (W1) (2024)
William Haese-Hill, Kathryn Crouch, Thomas Dan Otto
Annotation and visualization of parasite, fungi and arthropod genomes with Companion. Nucleic acids research 52 (W1) (2024)
Daniel W A Buchan, Lewis Moffat, Andy Lau, Shaun M Kandathil, David T Jones
Deep learning for the PSIPRED Protein Analysis Workbench. Nucleic acids research 52 (W1) (2024)
Antti Elonen, Leon Wimbes, Abdulmelik Mohammed, Pekka Orponen
DNAforge: a design tool for nucleic acid wireframe nanostructures. Nucleic acids research 52 (W1) (2024)
Zhiqiang Pang, Yao Lu, Guangyan Zhou, Fiona Hui, Lei Xu, Charles Viau, Aliya F Spigelman, Patrick E MacDonald, David S Wishart, Shuzhao Li, Jianguo Xia
MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation. Nucleic acids research 52 (W1) (2024)
Chih Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge. Nucleic acids research 52 (W1) (2024)
Natalia A Szulc, Filip Stefaniak, Małgorzata Piechota, Anna Soszyńska, Gabriela Piórkowska, Andrea Cappannini, Janusz M Bujnicki, Chiara Maniaci, Wojciech Pokrzywa
DEGRONOPEDIA: a web server for proteome-wide inspection of degrons. Nucleic acids research 52 (W1) (2024)