Works matching IS 03051048 AND DT 2024 AND VI 52 AND IP W1

Results: 77

Correction to 'ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery'.

Published in:: 2024
Publication type:: Correction Notice

The 22nd annual Nucleic Acids Research Web Server Issue 2024.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W1, doi. 10.1093/nar/gkae492

By:

Seelow, Dominik

Publication type:

Article

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'.

Published in:: 2024
Publication type:: Correction Notice

WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W415, doi. 10.1093/nar/gkae456

By:

Elizarraras, John M;
Liao, Yuxing;
Shi, Zhiao;
Zhu, Qian;
Pico, Alexander R;
Zhang, Bing

Publication type:

Article

ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W439, doi. 10.1093/nar/gkae424

By:

Shi, Shaohua;
Fu, Li;
Yi, Jiacai;
Yang, Ziyi;
Zhang, Xiaochen;
Deng, Youchao;
Wang, Wenxuan;
Wu, Chengkun;
Zhao, Wentao;
Hou, Tingjun;
Zeng, Xiangxiang;
Lyu, Aiping;
Cao, Dongsheng

Publication type:

Article

AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W187, doi. 10.1093/nar/gkae443

By:

Rubach, Pawel;
Sikora, Maciej;
Jarmolinska, Aleksandra I;
Perlinska, Agata P;
Sulkowska, Joanna I

Publication type:

Article

NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W108, doi. 10.1093/nar/gkae438

By:

Efimenko, Bogdan;
Popadin, Konstantin;
Gunbin, Konstantin

Publication type:

Article

Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W7, doi. 10.1093/nar/gkae433

By:

Li, Jinsen;
Rohs, Remo

Publication type:

Article

GCMS-ID: a webserver for identifying compounds from gas chromatography mass spectrometry experiments.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W381, doi. 10.1093/nar/gkae425

By:

Wakoli, Julia;
Anjum, Afia;
Sajed, Tanvir;
Oler, Eponine;
Wang, Fei;
Gautam, Vasuk;
LeVatte, Marcia;
Wishart, David S

Publication type:

Article

ChemFREE: a one-stop comprehensive platform for ecological and environmental risk evaluation of chemicals in one health world.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W450, doi. 10.1093/nar/gkae446

By:

Chen, Dongyu;
Liu, Yingwei;
Liu, Yang;
Zhao, Kejun;
Zhang, Tianhan;
Gao, Yangyang;
Wang, Qi;
Song, Baoan;
Hao, Gefei

Publication type:

Article

WeSA: a web server for improving analysis of affinity proteomics data.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W333, doi. 10.1093/nar/gkae423

By:

Shtetinska, Magdalena M;
González-Sánchez, Juan-Carlos;
Beyer, Tina;
Boldt, Karsten;
Ueffing, Marius;
Russell, Robert B

Publication type:

Article

SeqCAT: Sequence Conversion and Analysis Toolbox.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W116, doi. 10.1093/nar/gkae422

By:

Kornrumpf, Kevin;
Kurz, Nadine S;
Drofenik, Klara;
Krauß, Lukas;
Schneider, Carolin;
Koch, Raphael;
Beißbarth, Tim;
Dönitz, Jürgen

Publication type:

Article

MinActionPath2: path generation between different conformations of large macromolecular assemblies by action minimization.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W256, doi. 10.1093/nar/gkae421

By:

Koehl, Patrice;
Navaza, Rafael;
Tekpinar, Mustafa;
Delarue, Marc

Publication type:

Article

AggreProt: a web server for predicting and engineering aggregation prone regions in proteins.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W159, doi. 10.1093/nar/gkae420

By:

Planas-Iglesias, Joan;
Borko, Simeon;
Swiatkowski, Jan;
Elias, Matej;
Havlasek, Martin;
Salamon, Ondrej;
Grakova, Ekaterina;
Kunka, Antonín;
Martinovic, Tomas;
Damborsky, Jiri;
Martinovic, Jan;
Bednar, David

Publication type:

Article

AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W29, doi. 10.1093/nar/gkae419

By:

Rosignoli, Serena;
Lustrino, Elisa;
Conci, Alessio;
Fabrizi, Alessandra;
Rinaldo, Serena;
Latella, Maria Carmela;
Enzo, Elena;
Prosseda, Gianni;
De Rosa, Laura;
De Luca, Michele;
Paiardini, Alessandro

Publication type:

Article

CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W194, doi. 10.1093/nar/gkae415

By:

Ye, Bowei;
Tian, Wei;
Wang, Boshen;
Liang, Jie

Publication type:

Article

ProtVar: mapping and contextualizing human missense variation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W140, doi. 10.1093/nar/gkae413

By:

Stephenson, James D;
Totoo, Prabhat;
Burke, David F;
Jänes, Jürgen;
Beltrao, Pedro;
Martin, Maria J

Publication type:

Article

DDMut-PPI: predicting effects of mutations on protein–protein interactions using graph-based deep learning.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W207, doi. 10.1093/nar/gkae412

By:

Zhou, Yunzhuo;
Myung, YooChan;
Rodrigues, Carlos H M;
Ascher, David B

Publication type:

Article

TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W126, doi. 10.1093/nar/gkae411

By:

Li, Yuzhuo;
Lyu, Renzhe;
Chen, Shuai;
Wang, Yejun;
Sun, Ming-an

Publication type:

Article

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W83, doi. 10.1093/nar/gkae410

By:

Community, The Galaxy

Publication type:

Article

Proscan: a structure-based proline design web server.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W280, doi. 10.1093/nar/gkae408

By:

Felbinger, Nathaniel;
Ribeiro-Filho, Helder V;
Pierce, Brian G

Publication type:

Article

Next-generation IEDB tools: a platform for epitope prediction and analysis.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W526, doi. 10.1093/nar/gkae407

By:

Yan, Zhen;
Kim, Kevin;
Kim, Haeuk;
Ha, Brendan;
Gambiez, Anaïs;
Bennett, Jason;
de Almeida Mendes, Marcus Fabiano;
Trevizani, Raphael;
Mahita, Jarjapu;
Richardson, Eve;
Marrama, Daniel;
Blazeska, Nina;
Koşaloğlu-Yalçın, Zeynep;
Nielsen, Morten;
Sette, Alessandro;
Peters, Bjoern;
Greenbaum, Jason A

Publication type:

Article

MolModa: accessible and secure molecular docking in a web browser.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W498, doi. 10.1093/nar/gkae406

By:

Kochnev, Yuri;
Ahmed, Mayar;
Maldonado, Alex M;
Durrant, Jacob D

Publication type:

Article

REME: an integrated platform for reaction enzyme mining and evaluation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W299, doi. 10.1093/nar/gkae405

By:

Shi, Zhenkun;
Wang, Dehang;
Li, Yang;
Deng, Rui;
Lin, Jiawei;
Liu, Cui;
Li, Haoran;
Wang, Ruoyu;
Zhao, Muqiang;
Mao, Zhitao;
Yuan, Qianqian;
Liao, Xiaoping;
Ma, Hongwu

Publication type:

Article

SLiMAn 2.0: meaningful navigation through peptide-protein interaction networks.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W313, doi. 10.1093/nar/gkae398

By:

Reys, Victor;
Pons, Jean-Luc;
Labesse, Gilles

Publication type:

Article

AlphaFind: discover structure similarity across the proteome in AlphaFold DB.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W182, doi. 10.1093/nar/gkae397

By:

Procházka, David;
Slanináková, Terézia;
Olha, Jaroslav;
Rošinec, Adrián;
Grešová, Katarína;
Jánošová, Miriama;
Čillík, Jakub;
Porubská, Jana;
Svobodová, Radka;
Dohnal, Vlastislav;
Antol, Matej

Publication type:

Article

Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W481, doi. 10.1093/nar/gkae388

By:

Maier, Andreas;
Hartung, Michael;
Abovsky, Mark;
Adamowicz, Klaudia;
Bader, Gary D;
Baier, Sylvie;
Blumenthal, David B;
Chen, Jing;
Elkjaer, Maria L;
Garcia-Hernandez, Carlos;
Helmy, Mohamed;
Hoffmann, Markus;
Jurisica, Igor;
Kotlyar, Max;
Lazareva, Olga;
Levi, Hagai;
List, Markus;
Lobentanzer, Sebastian;
Loscalzo, Joseph;
Malod-Dognin, Noel

Publication type:

Article

SEMA 2.0: web-platform for B-cell conformational epitopes prediction using artificial intelligence.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W533, doi. 10.1093/nar/gkae386

By:

Ivanisenko, Nikita V;
Shashkova, Tatiana I;
Shevtsov, Andrey;
Sindeeva, Maria;
Umerenkov, Dmitriy;
Kardymon, Olga

Publication type:

Article

AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W176, doi. 10.1093/nar/gkae385

By:

Erdős, Gábor;
Dosztányi, Zsuzsanna

Publication type:

Article

PROSCA: an online platform for humanized scaffold mining facilitating rational protein engineering.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W272, doi. 10.1093/nar/gkae384

By:

Wang, Xiaona;
Zhang, Yintao;
Li, Zengpeng;
Duan, Zixin;
Guo, Menghan;
Wang, Zhen;
Zhu, Feng;
Xue, Weiwei

Publication type:

Article

LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W95, doi. 10.1093/nar/gkae383

By:

Zhang, Shikuan;
Wang, Songmao;
Lu, Fang;
Bie, Lingzi;
Luo, Yongjiang;
Sun, Jiahe;
Zhang, Yang;
Wang, Yi;
Zhang, Yaou;
Lyu, Qing Rex

Publication type:

Article

Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W170, doi. 10.1093/nar/gkae382

By:

Bárcenas, Oriol;
Kuriata, Aleksander;
Zalewski, Mateusz;
Iglesias, Valentín;
Pintado-Grima, Carlos;
Firlik, Grzegorz;
Burdukiewicz, Michał;
Kmiecik, Sebastian;
Ventura, Salvador

Publication type:

Article

GPSFun: geometry-aware protein sequence function predictions with language models.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W248, doi. 10.1093/nar/gkae381

By:

Yuan, Qianmu;
Tian, Chong;
Song, Yidong;
Ou, Peihua;
Zhu, Mingming;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

KinomeMETA: a web platform for kinome-wide polypharmacology profiling with meta-learning.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W489, doi. 10.1093/nar/gkae380

By:

Li, Zhaojun;
Qu, Ning;
Zhou, Jingyi;
Sun, Jingjing;
Ren, Qun;
Meng, Jingyi;
Wang, Guangchao;
Wang, Rongyan;
Liu, Jin;
Chen, Yijie;
Zhang, Sulin;
Zheng, Mingyue;
Li, Xutong

Publication type:

Article

Annotation and visualization of parasite, fungi and arthropod genomes with Companion.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W39, doi. 10.1093/nar/gkae378

By:

Haese-Hill, William;
Crouch, Kathryn;
Otto, Thomas D

Publication type:

Article

DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W54, doi. 10.1093/nar/gkae373

By:

Harris, Keith D;
Greenbaum, Gili

Publication type:

Article

DNAforge: a design tool for nucleic acid wireframe nanostructures.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W13, doi. 10.1093/nar/gkae367

By:

Elonen, Antti;
Wimbes, Leon;
Mohammed, Abdulmelik;
Orponen, Pekka

Publication type:

Article

REEV: review, evaluate and explain variants.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W148, doi. 10.1093/nar/gkae366

By:

Hramyka, Dzmitry;
Sczakiel, Henrike Lisa;
Zhao, Max Xiaohang;
Stolpe, Oliver;
Nieminen, Mikko;
Adam, Ronja;
Danyel, Magdalena;
Einicke, Lara;
Hägerling, René;
Knaus, Alexej;
Mundlos, Stefan;
Schwartzmann, Sarina;
Seelow, Dominik;
Ehmke, Nadja;
Mensah, Martin Atta;
Boschann, Felix;
Beule, Dieter;
Holtgrewe, Manuel

Publication type:

Article

Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W407, doi. 10.1093/nar/gkae364

By:

Hirsch, Pascal;
Molano, Leidy-Alejandra G;
Engel, Annika;
Zentgraf, Jens;
Rahmann, Sven;
Hannig, Matthias;
Müller, Rolf;
Kern, Fabian;
Keller, Andreas;
Schmartz, Georges P

Publication type:

Article

ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W45, doi. 10.1093/nar/gkae358

By:

Zou, Zhaonan;
Ohta, Tazro;
Oki, Shinya

Publication type:

Article

SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W368, doi. 10.1093/nar/gkae356

By:

Moafinejad, S Naeim;
de Aquino, Belisa R H;
Boniecki, Michał J;
Jeyeram, Iswarya P N Pandaranadar;
Nikolaev, Grigory;
Magnus, Marcin;
Farsani, Masoud Amiri;
Badepally, Nagendar Goud;
Wirecki, Tomasz K;
Stefaniak, Filip;
Bujnicki, Janusz M

Publication type:

Article

SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W362, doi. 10.1093/nar/gkae348

By:

Scholten, Niek R;
Haandrikman, Dennis;
Tolhuis, Joshua O;
Morandi, Edoardo;
Incarnato, Danny

Publication type:

Article

GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W238, doi. 10.1093/nar/gkae346

By:

Gou, Yujie;
Liu, Dan;
Chen, Miaomiao;
Wei, Yuxiang;
Huang, Xinhe;
Han, Cheng;
Feng, Zihao;
Zhang, Chi;
Lu, Teng;
Peng, Di;
Xue, Yu

Publication type:

Article

IsoVis – a webserver for visualization and annotation of alternative RNA isoforms.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W341, doi. 10.1093/nar/gkae343

By:

Wan, Ching Yin;
Davis, Jack;
Chauhan, Manveer;
Gleeson, Josie;
Prawer, Yair D J;
De Paoli-Iseppi, Ricardo;
Wells, Christine A;
Choi, Jarny;
Clark, Michael B

Publication type:

Article

RING 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W306, doi. 10.1093/nar/gkae337

By:

Del Conte, Alessio;
Camagni, Giorgia F;
Clementel, Damiano;
Minervini, Giovanni;
Monzon, Alexander Miguel;
Ferrari, Carlo;
Piovesan, Damiano;
Tosatto, Silvio C E

Publication type:

Article

Drawing human pedigree charts with DrawPed.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W61, doi. 10.1093/nar/gkae336

By:

Schönberger, Janina;
Steinhaus, Robin;
Seelow, Dominik

Publication type:

Article

LipidSig 2.0: integrating lipid characteristic insights into advanced lipidomics data analysis.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W390, doi. 10.1093/nar/gkae335

By:

Liu, Chia-Hsin;
Shen, Pei-Chun;
Lin, Wen-Jen;
Liu, Hsiu-Cheng;
Tsai, Meng-Hsin;
Huang, Tzu-Ya;
Chen, I-Chieh;
Lai, Yo-Liang;
Wang, Yu-De;
Hung, Mien-Chie;
Cheng, Wei-Chung

Publication type:

Article

Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W70, doi. 10.1093/nar/gkae331

By:

Forer, Lukas;
Taliun, Daniel;
LeFaive, Jonathon;
Smith, Albert V;
Boughton, Andrew P;
Coassin, Stefan;
Lamina, Claudia;
Kronenberg, Florian;
Fuchsberger, Christian;
Schönherr, Sebastian

Publication type:

Article

Deep learning for the PSIPRED Protein Analysis Workbench.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W287, doi. 10.1093/nar/gkae328

By:

Buchan, Daniel W A;
Moffat, Lewis;
Lau, Andy;
Kandathil, Shaun M;
Jones, David T

Publication type:

Article

ChemoDOTS: a web server to design chemistry-driven focused libraries.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W461, doi. 10.1093/nar/gkae326

By:

Hoffer, Laurent;
Charifi-Hoareau, Guillaume;
Barelier, Sarah;
Betzi, Stéphane;
Miller, Thomas;
Morelli, Xavier;
Roche, Philippe

Publication type:

Article