Developing Cybersecurity Systems Based on Machine Learning and Deep Learning Algorithms for Protecting Food Security Systems: Industrial Control Systems by Hasan Alkahtani, Theyazn H. H. Aldhyani

“…There were three types of attacks: man-in-the-middle (mitm) attack, web-server access attack, and telnet attack, as well as normal. …”
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High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus by Rim El Jeni, Kais Ghedira, Monia El Bour, Sonia Abdelhak, Alia Benkahla, Balkiss Bouhaouala-Zahar

“…The complete genome annotation was carried out with the Rapid Annotation using Subsystem Technology (RAST) web server then NCBI PGAAP. Results The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. …”
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Goober: A fully integrated and user-friendly microarray data management and analysis solution for core labs and bench biologists by Luo Wen, Gudipati Murali, Jung Kevin, Chen Mao, Marschke Keith B.

“…The whole package is freely available at http://sourceforge.net/projects/goober. A demo web server is available at http://www.goober-array.org.…”
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Dynamic Expression of Novel MiRNA Candidates and MiRNA-34 Family Members in Early- to Mid-Gestational Fetal Keratinocytes Contributes to Scarless Wound Healing by Targeting the TGF... by Feng Zhao, Zhe Wang, Hongxin Lang, Xiaoyu Liu, Dianbao Zhang, Xiliang Wang, Tao Zhang, Rui Wang, Ping Shi, Xining Pang

“…To uncover potential novel microRNA (miRNAs), the mirTools 2.0 web server was used to identify candidate novel human miRNAs from the NGS data. …”
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4mCpred-EL: An Ensemble Learning Framework for Identification of DNA <i>N⁴</i>-Methylcytosine Sites in the Mouse Genome by Balachandran Manavalan, Shaherin Basith, Tae Hwan Shin, Da Yeon Lee, Leyi Wei, Gwang Lee

“…We provided a user-friendly web server, namely 4mCpred-EL which could be implemented as a pre-screening tool for the identification of potential 4mC sites in the mouse genome.…”
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Prophage Carriage and Genetic Diversity within Environmental Isolates of <i>Clostridioides difficile</i> by Khald Blau, Claudia Gallert

“…Predicted prophages and CRISPR-Cas systems were identified by using the PHASTER web server and CRISPRCasFinder, respectively. Phylogenetic relationships among predicated prophages were also constructed based on phage-related genes, terminase large (TerL) subunits and LysM. …”
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iProm-Sigma54: A CNN Base Prediction Tool for <i>σ</i>⁵⁴ Promoters by Muhammad Shujaat, Hoonjoo Kim, Hilal Tayara, Kil To Chong

“…Additionally, a publicly accessible web server was constructed.…”
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Peptide Utility (PU) search server: A new tool for peptide sequence search from multiple databases by Tanishq Chamoli, Alisha Khera, Akanksha Sharma, Anshul Gupta, Sonam Garg, Kanishk Mamgain, Aayushi Bansal, Shriya Verma, Ankit Gupta, Hema K. Alajangi, Gurpal Singh, Ravi P. Barnwal

“…To overcome these limitations, a user-friendly interface, the Peptide Utility (PU) webserver (https://chain-searching.herokuapp.com/) has been developed for searching and analyzing homologous and identical protein/peptide sequences that can be searched from approximately 0.4 million sequences (structural and sequence information) in both online and offline modes. The PU web server can also be used to study different types of interactions in PDBSum, identifying the most dominating interface residues, the most prevalent interactions, and the interaction preferences of different residues. …”
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The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses by Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva

“…Also available as a web server, CONSRANK ranks docking models in an ensemble based on their ability to match the most frequent inter-residue contacts in it. …”
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iRNA-m2G: Identifying N2-methylguanosine Sites Based on Sequence-Derived Information by Wei Chen, Xiaoming Song, Hao Lv, Hao Lin

“…Keywords: N2-methylguanosine, nucleotide chemical property, accumulated nucleotide frequency, web server…”
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TCM2COVID: A resource of anti‐COVID‐19 traditional Chinese medicine with effects and mechanisms by Liping Ren, Yi Xu, Lin Ning, Xianrun Pan, Yuchen Li, Qi Zhao, Bo Pang, Jian Huang, Kejun Deng, Yang Zhang

“…The current version of TCM2COVID (1) documents over 280 TCM formulas (including over 300 herbs) with detailed clinical evidence and therapeutic mechanism information; (2) records over 80 NPs with detailed potential therapeutic mechanisms; and (3) launches a useful web server for querying, analyzing and visualizing documented formulas similar to those supplied by the user (formula similarity analysis). …”
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Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods by Chaofeng Lou, Hongbin Yang, Hua Deng, Mengting Huang, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang

“…To facilitate the use of these mutagenicity transformation rules, we integrated them into ADMETopt2 ( http://lmmd.ecust.edu.cn/admetsar2/admetopt2/ ), a free web server for optimization of chemical ADMET properties. …”
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Introduction of protein vaccine candidate based on AP65, AP33, and α-actinin proteins against Trichomonas vaginalis parasite: an immunoinformatics design by Forozan Ghasemi Nezhad, Afsaneh Karmostaji, Parisa Sarkoohi, Behzad Shahbazi, Zahra Gharibi, Batul Negahdari, Khadijeh Ahmadi

“…Investigation of the ability of the designed protein to induce an immune response using the C-ImmSim web server also showed that the designed protein is capable of stimulating B- and T-cell lymphocytes to produce the necessary cytokines and antibodies against Trichomonas vaginalis. …”
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A Web Resource for Designing Subunit Vaccine Against Major Pathogenic Species of Bacteria by Gandharva Nagpal, Gandharva Nagpal, Salman Sadullah Usmani, Salman Sadullah Usmani, Gajendra P. S. Raghava, Gajendra P. S. Raghava

“…In order to provide service to scientific community, we developed a web server VacTarBac for designing of vaccines against above species of bacteria. …”
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SAAMBE-3D: Predicting Effect of Mutations on Protein–Protein Interactions by Swagata Pahari, Gen Li, Adithya Krishna Murthy, Siqi Liang, Robert Fragoza, Haiyuan Yu, Emil Alexov

“…SAAMBE-3D is available as a web server and as well as a stand-alone code, the last one being another important feature allowing other researchers to directly download the code and run it on their local computer. …”
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DeepNeuropePred: A robust and universal tool to predict cleavage sites from neuropeptide precursors by protein language model by Lei Wang, Zilu Zeng, Zhidong Xue, Yan Wang

“…For the convenience of researchers, we provide a web server (http://isyslab.info/NeuroPepV2/deepNeuropePred.jsp).…”
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Evaluation of Lipin 1 polymorphisms for genetic markers in association with performance traits in Azikheli buffalo by Muhammad Siraj, Muhammad Ibrahim, Bibi Sabiha, Sohail Ahmad

“…Moreover, the visualization of 3D structure of the lipin I protein constructed using Phyr2 web server and the Missense 3D analysis identified no structural damages caused by the reported SNPs on the target protein. …”
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PredPS: Attention-based graph neural network for predicting stability of compounds in human plasma by Woo Dae Jang, Jidon Jang, Jin Sook Song, Sunjoo Ahn, Kwang-Seok Oh

“…The source code for PredPS is available at https://bitbucket.org/krict-ai/predps and the PredPS web server is available at https://predps.netlify.app.…”
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Remote poultry management system for small to medium scale producers using IoT by Justice Chigwada, Felix Mazunga, Cloud Nyamhere, Victor Mazheke, Nicholas Taruvinga

“…A “cron job” enables the web server to perform repetitive and specific tasks at specific times. …”
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Deep-WET: a deep learning-based approach for predicting DNA-binding proteins using word embedding techniques with weighted features by S. M. Hasan Mahmud, Kah Ong Michael Goh, Md. Faruk Hosen, Dip Nandi, Watshara Shoombuatong

“…This superior performance shows that Deep-WET has a tremendous predictive capacity to predict DBPs. The web server of Deep-WET and curated datasets in this study are available at https://deepwet-dna.monarcatechnical.com/ . …”
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