Nucleic Acids Res.

Keyphrases

Publications

volume 51, number W1, 2023

Arthur Declercq, Robbin Bouwmeester, Cristina Chiva, Eduard Sabidó, Aurélie Hirschler, Christine Carapito, Lennart Martens, Sven Degroeve, Ralf Gabriels
Updated MS²PIP web server supports cutting-edge proteomics applications. Nucleic Acids Res. 51 (W1) (2023)
Sushmita Basu, Jörg Gsponer, Lukasz A. Kurgan
DEPICTER2: a comprehensive webserver for intrinsic disorder and disorder function prediction. Nucleic Acids Res. 51 (W1) (2023)
Kai Liu, Xufeng Lu, Hang Shi, Xiaojun Xu, Ren Kong, Shan Chang
nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands. Nucleic Acids Res. 51 (W1) (2023)
Qianqian Song, Mingyu Li, Qian Li, Xun Lu, Kun Song, Ziliang Zhang, Jiale Wei, Liang Zhang, Jiacheng Wei, Youqiong Ye, Jinyin Zha, Qiufen Zhang, Qiang Gao, Jiang Long, Xinyi Liu, Xuefeng Lu, Jian Zhang
DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations. Nucleic Acids Res. 51 (W1) (2023)
Xing-Xing Shi, Zhi-Zheng Wang, Fan Wang, Ge-Fei Hao, Guangfu Yang
ACFIS 2.0: an improved web-server for fragment-based drug discovery via a dynamic screening strategy. Nucleic Acids Res. 51 (W1) (2023)
Yanhui Hu, Aram Comjean, Helen Attrill, Giulia Antonazzo, Jim Thurmond, Weihang Chen, Fangge Li, Tiffany Chao, Stephanie E. Mohr, Nicholas H. Brown, Norbert Perrimon
and common research organisms. Nucleic Acids Res. 51 (W1) (2023)
Volodymyr Tsybulskyi, Egor Semenchenko, Irmtraud M. Meyer
e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features. Nucleic Acids Res. 51 (W1) (2023)
Liam J. McGuffin, Nicholas S. Edmunds, Ahmet G. Genc, Shuaa M. A Alharbi, Bajuna R. Salehe, Recep Adiyaman
Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers. Nucleic Acids Res. 51 (W1) (2023)
Kai Blin, Simon Shaw, Hannah E. Augustijn, Zachary L. Reitz, Friederike Biermann, Mohammad Alanjary, Artem Fetter, Barbara R. Terlouw, William W. Metcalf, Eric J. N. Helfrich, Gilles P. van Wezel, Marnix H. Medema, Tilmann Weber
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res. 51 (W1) (2023)
David S. Wishart, Scott Han, Sukanta Saha, Eponine Oler, Harrison Peters, Jason R. Grant, Paul Stothard, Vasuk Gautam
PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res. 51 (W1) (2023)
Ondrej Schindler, Karel Berka, Alessio Cantara, Ales Krenek, Dominik Tichý, Tomás Racek, Radka Svobodová Vareková
αCharges: partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Res. 51 (W1) (2023)
Lukasz Ciecierski, Ireneusz Stolarek, Marek Figlerowicz
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics. Nucleic Acids Res. 51 (W1) (2023)
Alla Mikheenko, Vladislav Saveliev, Pascal Hirsch, Alexey A. Gurevich
WebQUAST: online evaluation of genome assemblies. Nucleic Acids Res. 51 (W1) (2023)
Hao Tian, Sian Xiao, Xi Jiang, Peng Tao
PASSer: fast and accurate prediction of protein allosteric sites. Nucleic Acids Res. 51 (W1) (2023)
Ernesto Aparicio-Puerta, Pascal Hirsch, Georges Pierre Schmartz, Fabian Kern, Tobias Fehlmann, Andreas Keller
miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations. Nucleic Acids Res. 51 (W1) (2023)
Rémi Gschwind, Svetlana Ugarcina perovic, Maja Weiss, Marie Petitjean, Julie Lao, Luís Pedro Coelho, Etienne Ruppé
ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics. Nucleic Acids Res. 51 (W1) (2023)
Potdar Swapnil, Filipp Ianevski, Aleksandr Ianevski, ZiaurRehman Tanoli, Krister Wennerberg, Brinton Seashore-Ludlow, Olli-P. Kallioniemi, Päivi Östling, Tero Aittokallio, Saarela Jani
Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data. Nucleic Acids Res. 51 (W1) (2023)
Jason R. Grant, Eric Enns, Eric Marinier, Arnab Mandal, Emily K. Herman, Chih-yu Chen, Morag Graham, Gary H. Van Domselaar, Paul Stothard
Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res. 51 (W1) (2023)
Jinfang Zheng, Qiwei Ge, Yuchen Yan, Xinpeng Zhang, Le Huang, Yanbin Yin
dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res. 51 (W1) (2023)
Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, Alex S. Holehouse, Daniel A. Griffith, Ryan J. Emenecker, Ashwini Patil, Ronesh Sharma, Tatsuhiko Tsunoda, Alok Sharma, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 51 (W1) (2023)
Jiahe Sun, Fang Lu, Yongjiang Luo, Lingzi Bie, Ling Xu, Yi Wang
OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res. 51 (W1) (2023)
Rui Yin, Helder Veras Ribeiro filho, Valerie Lin, Ragul Gowthaman, Melyssa Cheung, Brian G. Pierce
TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning. Nucleic Acids Res. 51 (W1) (2023)
Dominik Seelow
Web Server Issue 2023. Nucleic Acids Res. 51 (W1) (2023)
Yiran Xu, Jianghui Zhu, Wenze Huang, Kui Xu, Rui Yang, Qiangfeng Cliff Zhang, Lei Sun
RNA structural information. Nucleic Acids Res. 51 (W1) (2023)
David S. Wishart, Leah Ren, Jacques Leong-Sit, Sukanta Saha, Jason R. Grant, Paul Stothard, Upasana Singh, Abby Kropielnicki, Eponine Oler, Harrison Peters, Vasuk Gautam
PlasMapper 3.0 - a web server for generating, editing, annotating and visualizing publication quality plasmid maps. Nucleic Acids Res. 51 (W1) (2023)
Chaohui Bao, Shan Wang, Lulu Jiang, Zhongcheng Fang, Kexin Zou, James Lin, Saijuan Chen, Hai Fang
OpenXGR: a web-server update for genomic summary data interpretation. Nucleic Acids Res. 51 (W1) (2023)
Yuexu Jiang, Lei Jiang, Chopparapu Sai Akhil, Duolin Wang, Ziyang Zhang, Weinan Zhang, Dong Xu
MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels. Nucleic Acids Res. 51 (W1) (2023)
María José Jiménez-Santos, Alba Nogueira-Rodríguez, Elena Piñeiro-Yáñez, Hugo López-Fernández, Santiago García-Martín, Paula Gómez-Plana, Miguel Reboiro-Jato, Gonzalo Gómez-López, Daniel Glez-Peña, Fátima Al-Shahrour
PanDrugs2: prioritizing cancer therapies using integrated individual multi-omics data. Nucleic Acids Res. 51 (W1) (2023)
Kristian Barrett, Cameron J. Hunt, Lene Lange, Igor V. Grigoriev, Anne S. Meyer
Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes. Nucleic Acids Res. 51 (W1) (2023)
Spyros Tastsoglou, Giorgos Skoufos, Marios Miliotis, Dimitra Karagkouni, Ioannis Koutsoukos, Anna Karavangeli, Filippos S. Kardaras, Artemis G. Hatzigeorgiou
DIANA-miRPath v4.0: expanding target-based miRNA functional analysis in cell-type and tissue contexts. Nucleic Acids Res. 51 (W1) (2023)
Spyros Tastsoglou, Athanasios Alexiou, Dimitra Karagkouni, Giorgos Skoufos, Elissavet Zacharopoulou, Artemis G. Hatzigeorgiou
DIANA-microT 2023: including predicted targets of virally encoded miRNAs. Nucleic Acids Res. 51 (W1) (2023)
Christoph Elfmann, Jörg Stülke
PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks. Nucleic Acids Res. 51 (W1) (2023)
Jeong Yeon Kim, Hyoeun Bang, Seung-Jae Noh, Jung Kyoon Choi
DeepNeo: a webserver for predicting immunogenic neoantigens. Nucleic Acids Res. 51 (W1) (2023)
Tomasz Wozniak, Weronika Sura, Marta Kazimierska, Marta elzbieta Kasprzyk, Marta Podralska, Agnieszka Dzikiewicz-Krawczyk
TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs. Nucleic Acids Res. 51 (W1) (2023)
Dávid Bajusz, Gáspár Pándy-Szekeres, Ágnes Takács, Elvin D. de araujo, György M. Keserü
SH2db, an information system for the SH2 domain. Nucleic Acids Res. 51 (W1) (2023)
Joshua S. Martin Beem, Sravani Venkatayogi, Barton F. Haynes, Kevin Wiehe
ARMADiLLO: a web server for analyzing antibody mutation probabilities. Nucleic Acids Res. 51 (W1) (2023)
Xiangshang Li, Chunfu Xiao, Juntian Qi, Weizhen Xue, Xinwei Xu, Zelin Mu, Jie Zhang, Chuan-Yun Li, Wanqiu Ding
STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data. Nucleic Acids Res. 51 (W1) (2023)
Bartosz Adamczyk, Michal Zurkowski, Marta Szachniuk, Tomasz Zok
WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures. Nucleic Acids Res. 51 (W1) (2023)
Véronique Geoffroy, Jean-Baptiste Lamouche, Thomas Guignard, Samuel Nicaise, Arnaud Kress, Sophie Scheidecker, Antony Le Béchec, Jean Muller
The AnnotSV webserver in 2023: updated visualization and ranking. Nucleic Acids Res. 51 (W1) (2023)
Javier López-Ibáñez, Florencio Pazos, Monica Chagoyen
MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis. Nucleic Acids Res. 51 (W1) (2023)
Philip Z. Johnson, Anne E. Simon
RNAcanvas: interactive drawing and exploration of nucleic acid structures. Nucleic Acids Res. 51 (W1) (2023)
Tianyi Qiu, Lu Zhang, Zikun Chen, Yuan Wang, Tiantian Mao, Caicui Wang, Yewei Cun, Genhui Zheng, Deyu Yan, Mengdi Zhou, Kailin Tang, Zhiwei Cao
SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs. Nucleic Acids Res. 51 (W1) (2023)
Fengcui Qian, Li-Wei Zhou, Yanyu Li, Zhengmin Yu, Li-Dong Li, Yuezhu Wang, Mingcong Xu, Qiuyu Wang, Chunquan Li
SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse. Nucleic Acids Res. 51 (W1) (2023)
Ferdous Nasri, Kunaphas Kongkitimanon, Alice Wittig, Jorge Sánchez Cortés, Annika Brinkmann, Andreas Nitsche, Anna-Juliane Schmachtenberg, Bernhard Y. Renard, Stephan Fuchs
MpoxRadar: a worldwide MPXV genomic surveillance dashboard. Nucleic Acids Res. 51 (W1) (2023)
Jinyin Zha, Qian Li, Xinyi Liu, Weidong Lin, Tingting Wang, Jiacheng Wei, Ziliang Zhang, Xun Lu, Jing Wu, Duan Ni, Kun Song, Liang Zhang, Xuefeng Lu, Shaoyong Lu, Jian Zhang
AlloReverse: multiscale understanding among hierarchical allosteric regulations. Nucleic Acids Res. 51 (W1) (2023)
Simon Mendelsohn, David Froelicher, Denis Loginov, David Bernick, Bonnie Berger, Hyunghoon Cho
sfkit: a web-based toolkit for secure and federated genomic analysis. Nucleic Acids Res. 51 (W1) (2023)
Anastasija Zaiko, Maximilian Scheel, Jessica Schattschneider, Ulla von Ammon, Michelle Scriver, Xavier Pochon, John K. Pearman
Pest Alert Tool - a web-based application for flagging species of concern in metabarcoding datasets. Nucleic Acids Res. 51 (W1) (2023)
João Victor da Silva Guerra, Helder Veras Ribeiro filho, José Geraldo de Carvalho Pereira, Paulo Sérgio Lopes-de-Oliveira
KVFinder-web: a web-based application for detecting and characterizing biomolecular cavities. Nucleic Acids Res. 51 (W1) (2023)
Fengxia Zhou, Xiaorong Yu, Rui Gan, Kuan Ren, Chuangeng Chen, Chunyan Ren, Meng Cui, Yuchen Liu, Yiyang Gao, Shouyu Wang, Mingyu Yin, Tengjin Huang, Zhiwei Huang, Fan Zhang
CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing. Nucleic Acids Res. 51 (W1) (2023)
Sebastian Schönherr, Hansi Weißensteiner, Florian Kronenberg, Lukas Forer
Haplogrep 3 - an interactive haplogroup classification and analysis platform. Nucleic Acids Res. 51 (W1) (2023)