LncCat: An ORF attention model to identify LncRNA based on ensemble learning strategy and fused sequence information by Hongqi Feng, Shaocong Wang, Yan Wang, Xinye Ni, Zexi Yang, Xuemei Hu, Sen Yang

“…Additionally, a user-friendly web server is developed for academics at http://cczubio.top/lnccat.…”
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Genomic delineation and description of species and within-species lineages in the genus Pantoea by Katherine C. Crosby, Mariah Rojas, Parul Sharma, Parul Sharma, Marcela A. Johnson, Marcela A. Johnson, Reza Mazloom, Brian H. Kvitko, Theo H. M. Smits, Stephanus N. Venter, Teresa A. Coutinho, Teresa A. Coutinho, Lenwood S. Heath, Marike Palmer, Marike Palmer, Boris A. Vinatzer

“…Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.…”
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Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB) by Antoni Hermoso, Jordi Espadaler, E Enrique Querol, Francesc X. Aviles, Michael J.E. Sternberg, Baldomero Oliva, Narcis Fernandez-Fuentes

“…All this information and the possibility to browse/query the database through a web-server outline an useful tool with application in the comparative study of loops, the analysis of loops involved in protein function and to obtain templates for loop modeling.…”
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Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. by Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu

“…In the recent blind CAMEO benchmark, our fully-automated web server implementing this method successfully folded 6 targets with a new fold and only 0.3L-2.3L effective sequence homologs, including one β protein of 182 residues, one α+β protein of 125 residues, one α protein of 140 residues, one α protein of 217 residues, one α/β of 260 residues and one α protein of 462 residues. …”
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Novel ADAMTS13 mutations in a patient with congenital thrombotic thrombocytopenic purpura by Zhitao Wang, Xinhui Zhang, Xueqin Lu, Peng Peng, Huiru Wang, Shanglong Feng, Li Zhou

“…The 3D structures of the natural and mutated ADAMTS-13 proteins were partially reconstructed using the Phyre2 web server. The mutation that replaces the tyrosine residue at amino acid position 177 with cysteine may result in decreased steric hindrance and a looser structure. …”
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FastD: Fast detection of insecticide target‐site mutations and overexpressed detoxification genes in insect populations from RNA‐Seq data by Longfei Chen, Kun Lang, Yang Mei, Zhenmin Shi, Kang He, Fei Li, Huamei Xiao, Gongyin Ye, Zhaojun Han

“…Then, we developed a Perl program, FastD, to detect target‐site mutations and overexpressed detoxification genes from RNA‐Seq data and constructed a web server for FastD (http://www.insect-genome.com/fastd). …”
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POOE: predicting oomycete effectors based on a pre-trained large protein language model by Miao Zhao, Chenping Lei, Kewei Zhou, Yan Huang, Chen Fu, Shiping Yang, Ziding Zhang

“…We anticipate that POOE can accelerate the identification of oomycete effectors and provide new hints to systematically understand the functional roles of effectors in plant–pathogen interactions. The web server of POOE is freely accessible at http://zzdlab.com/pooe/index.php. …”
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Ion-pumping microbial rhodopsin protein classification by machine learning approach by Muthu Krishnan Selvaraj, Anamika Thakur, Manoj Kumar, Anil Kumar Pinnaka, Chander Raman Suri, Busi Siddhardha, Senthil Prasad Elumalai

“…Apart from this study, we also tested the own, blank, BLAST dataset and annotated whole-genome rhodopsin sequences of PWS haloarchaeal isolates in the developed methods. The developed web server ( https://bioinfo.imtech.res.in/servers/rhodopred ) can identify the Ion Pumping Haloarchaeal rhodopsin proteins and their subtypes. …”
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Designing and usability assessing an electronic personal health record for patients with chronic heart failure in a developing country by Mehrdad Farzandipour, Ehsan Nabovati, Alireza Farrokhian, Hossein Akbari, Fatemeh Rezaei hasanvand, Reihane Sharif

“…Then the system was designed and developed using the PHP programing language and MySQL database server and implemented on a web server. The system's usability was assessed by three cardiologists and three patients using the System Usability Scale (SUS) questionnaire and five health information technology experts using Nielsen's usability heuristics. …”
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An Effective Integrated Machine Learning Framework for Identifying Severity of Tomato Yellow Leaf Curl Virus and Their Experimental Validation by Nattanong Bupi, Vinoth Kumar Sangaraju, Le Thi Phan, Aamir Lal, Thuy Thi Bich Vo, Phuong Thi Ho, Muhammad Amir Qureshi, Marjia Tabassum, Sukchan Lee, Balachandran Manavalan

“…Plant virologists and plant breeding professionals can access the user-friendly online IML-TYLCVs web server at https://balalab-skku.org/IML-TYLCVs, which can guide them in developing new protection strategies for newly emerging viruses.…”
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Argonaut: A Web Platform for Collaborative Multi-omic Data Visualization and Exploration by Dain R. Brademan, Ian J. Miller, Nicholas W. Kwiecien, David J. Pagliarini, Michael S. Westphall, Joshua J. Coon, Evgenia Shishkova

“…However, developing these tailored companion resources requires programming expertise and knowledge of web server architecture—a substantial burden for most. …”
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LAITOR4HPC: A text mining pipeline based on HPC for building interaction networks by Bruna Piereck, Marx Oliveira-Lima, Ana Maria Benko-Iseppon, Sarah Diehl, Reinhard Schneider, Ana Christina Brasileiro-Vidal, Adriano Barbosa-Silva

“…PESCADOR is an online web server based on LAITOR and NLProt text mining tools, which retrieves protein-protein co-occurrences in a tabular-based format, adding a network schema. …”
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maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination by Nashar Karim, Wood A Joseph, Hulme Helen, Hayes Andrew, Morrison Norman, Velarde Giles, Wilson Michael, Hancock David, Kell Douglas B, Brass Andy

“…</p> <p>maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. …”
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A Yes-Associated Protein (YAP) and Insulin-Like Growth Factor 1 Receptor (IGF-1R) Signaling Loop Is Involved in Sorafenib Resistance in Hepatocellular Carcinoma by Mai-Huong T. Ngo, Sue-Wei Peng, Yung-Che Kuo, Chun-Yen Lin, Ming-Heng Wu, Chia-Hsien Chuang, Cheng-Xiang Kao, Han-Yin Jeng, Gee-Way Lin, Thai-Yen Ling, Te-Sheng Chang, Yen-Hua Huang

“…Different cancer cell lines from databases were analyzed through the ONCOMINE web server. BIOSTORM–LIHC patient tissues (46 nonresponders and 21 responders to sorafenib) were used to compare YAP mRNA levels. …”
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Sistema de informação dos núcleos de atenção integral na saúde da família - SINAI Information system of integral assistance nuclei in family health (SINAI) by Mirella Maria Soares Véras, Paulo Henrique Dias Quinderé, Luciano Parente Ferreira, Jeovânia Maria Goersch Andrade Aragão, Maria Abigail Aguiar Arruda Coelho

“…The operational system used was Linux, PHP language, POSTGRESQL database, and it is accommodated on an APACHE web server. The system was called SINAI at the beginning and provides important data for the development of indicators by various professionals, guaranteeing the production of epidemical information necessary for the process of control, evaluation and planning of team actions.…”
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Positive-unlabelled learning of glycosylation sites in the human proteome by Fuyi Li, Yang Zhang, Anthony W. Purcell, Geoffrey I. Webb, Kuo-Chen Chou, Trevor Lithgow, Chen Li, Jiangning Song

“…In addition, we developed an online web server as an implementation of the optimized model (available at http://glycomine.erc.monash.edu/Lab/GlycoMine_PU/) to facilitate community-wide efforts for accurate prediction of protein glycosylation sites. …”
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Induction of antimicrobial, antioxidant metabolites production by co-cultivation of two red-sea-sponge-associated Aspergillus sp. CO2 and Bacillus sp. COBZ21 by Ahmed A. Hamed, Mosad A. Ghareeb, Ayda K. Kelany, Mohamed Abdelraof, Hoda A. Kabary, Nariman R. Soliman, Mohamed E. Elawady

“…The toxicity prediction of the coculture extract was performed using the ProTox II web server, which showed that the selected compound has no pronounced toxicity.…”
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A Comprehensive Approach to Derivatization: Elemental Composition, Biochemical, and In Silico Studies of Metformin Derivatives Containing Copper and Zinc Complexes by Javed Ahmed, Mohsin Abbas Khan, Muhammad Ehsan Khalid, Irshad Ahmad, Irfan Pervaiz, Umair Khurshid, Saharish Khaliq, Kashif ur Rehman Khan, Muhammad Adeel Arshad, Ghadeer M. Albadrani, Ahmed E. Altyar, Amany A. Sayed, Mousa O. Germoush, Mohamed M. Abdel-Daim

“…The Swiss ADME online web server was utilized to compute ADME properties of metformin analogues. …”
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Experience sharing web application by Zhou, Fengyi

“…The next chapter discussed the detailed design and implementation from font-end, web server to back-end based on the defined software requirements in previous chapter. …”
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NeisseriaBase: A specialised Neisseria genomic resource and analysis platform by Zheng, W., Mutha, N.V.R., Heydari, H., Dutta, A., Siow, C.C., Jakubovics, N.S., Wee, W.Y., Tan, S.Y., Ang, M.Y., Wong, G.J., Choo, S.W.

“…The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. …”