DeepMPF: deep learning framework for predicting drug–target interactions based on multi-modal representation with meta-path semantic analysis by Zhong-Hao Ren, Zhu-Hong You, Quan Zou, Chang-Qing Yu, Yan-Fang Ma, Yong-Jian Guan, Hai-Ru You, Xin-Fei Wang, Jie Pan

“…It can be utilized as a useful tool to prescreen the most potential drug candidates for the protein. The web server of the DeepMPF predictor is freely available at http://120.77.11.78/DeepMPF/ , which can help relevant researchers to further study.…”
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ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data by Dianhao Guo, Jiapeng Luo, Yuenan Zhou, Huamei Xiao, Kang He, Chuanlin Yin, Jianhua Xu, Fei Li

“…Known ace resistance mutations were collected and used as a reference. We constructed a Web server for ACE, and the standalone software in both Linux and Windows versions is available for download. …”
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Neuropsychiatric Symptoms of COVID-19 Explained by SARS-CoV-2 Proteins’ Mimicry of Human Protein Interactions by Hale Yapici-Eser, Hale Yapici-Eser, Yunus Emre Koroglu, Yunus Emre Koroglu, Ozgur Oztop-Cakmak, Ozgur Oztop-Cakmak, Ozlem Keskin, Ozlem Keskin, Attila Gursoy, Attila Gursoy, Yasemin Gursoy-Ozdemir, Yasemin Gursoy-Ozdemir

“…HMI-PRED (Host-Microbe Interaction PREDiction), a recently developed web server for structural PREDiction of protein-protein interactions (PPIs) between host and any microbial species, was used to find the “interface mimicry” through which the microbial proteins hijack host binding surfaces. …”
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DeepSecE: A Deep-Learning-Based Framework for Multiclass Prediction of Secreted Proteins in Gram-Negative Bacteria by Yumeng Zhang, Jiahao Guan, Chen Li, Zhikang Wang, Zixin Deng, Robin B. Gasser, Jiangning Song, Hong-Yu Ou

“…The present analysis demonstrates that DeepSecE has major potential for the discovery of disease-associated secreted proteins in a diverse range of Gram-negative bacteria. An online web server of DeepSecE is also publicly available to predict and explore various secreted substrate proteins via the input of bacterial genome sequences.…”
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GeneCloudOmics: A Data Analytic Cloud Platform for High-Throughput Gene Expression Analysis by Mohamed Helmy, Mohamed Helmy, Rahul Agrawal, Javed Ali, Mohamed Soudy, Thuy Tien Bui, Kumar Selvarajoo, Kumar Selvarajoo, Kumar Selvarajoo

“…Here we present GeneCloudOmics, an easy-to-use web server for high-throughput gene expression analysis that extends the functionality of our previous ABioTrans with several new tools, including protein datasets analysis, and a web interface. …”
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Identification and Biological Evaluation of CK2 Allosteric Fragments through Structure-Based Virtual Screening by Chunqiong Li, Xuewen Zhang, Na Zhang, Yue Zhou, Guohui Sun, Lijiao Zhao, Rugang Zhong

“…The ChemBridge fragment library was searched by evaluating the fit values of these molecules with the optimized pharmacophore model, as well as the binding affinity of the CK2α-ligand complexes predicted by Alloscore web server. Six hits forming the holistic interaction mechanism with the αD pocket were retained after pharmacophore- and Alloscore-based screening for biological test. …”
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MTTLm⁶A: A multi-task transfer learning approach for base-resolution mRNA m⁶A site prediction based on an improved transformer by Honglei Wang, Wenliang Zeng, Xiaoling Huang, Zhaoyang Liu, Yanjing Sun, Lin Zhang

“…To enhance user convenience, we have made a user-friendly web server for MTTLm⁶A publicly available at <a target="_blank" xmlns:xlink="http://www.w3.org/1999/xlink" href="http://47.242.23.141/MTTLm6A/index.php">http://47.242.23.141/MTTLm6A/index.php…”
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Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis by Mansour K. Gatasheh, Sathan Raj Natarajan, Rajapandiyan Krishnamoorthy, Tawfiq S Alsulami, Ponnulakshmi Rajagopal, Chella Perumal Palanisamy, Vishnu Priya Veeraraghavan, Selvaraj Jayaraman

“…To gain insights into the functional roles of these hub genes, gene ontology and pathway enrichment were conducted thorough g: profiler web server. Subsequently, overall survival plots from GEPIA and oncogenic predictive functions like mRNA expressions for stages and nodal metastasis were employed to identify hub genes in CRC patient samples. …”
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Molecular docking study of sea urchin (Arbacia lixula) peptides as multi-target inhibitor for non-small cell lung cancer (NSCLC) associated proteins. by Muhammad Hermawan Widyananda, Setyaki Kevin Pratama, Rizky Senna Samoedra, Fikriya Novita Sari, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Yulanda Antonius

“…Methods: Peptide modeling was performed using the PEP-FOLD3 web server. Proteins that have a crucial role in NSCLC progression were determined using KEGG pathway database. 3D protein structures such as EGFR, PI3K, BRAF V600E, and JAK3 were taken from the RCSB PDB database. …”
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In silico Study of Antiviral Activity of Polyphenol Compounds from Ocimum basilicum by Molecular Docking, ADMET, and Drug-Likeness Analysis by Kurnia D, Putri SA, Tumilaar SG, Zainuddin A, Dharsono HDA, Amin MF

“…Apigenin-7-glucuronide, dihydrokaempferol-3-glucoside, and aesculetin are polyphenolic compounds found in Ocimum basilicum.Purpose: The purpose of this study was to analyze the mechanism of inhibition of the three polyphenolic compounds in Ocimum basilicum against the main protease and to predict pharmacokinetic activity and the drug-likeness of a compound using the Lipinski Rule of Five.Patients and Methods: The method used is to predict the molecular docking inhibition mechanism using Autodock 4.0 tools and use pkcsm and protox online web server to analyze ADMET and Drug-likeness.Results: The binding affinity for apigenin-7-glucuronide was − 8.77 Kcal/mol, dihydrokaempferol-3-glucoside was − 8.96 Kcal/mol, and aesculetin was − 5.79 Kcal/mol. …”
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Computational method using heterogeneous graph convolutional network model combined with reinforcement layer for MiRNA–disease association prediction by Dan Huang, JiYong An, Lei Zhang, BaiLong Liu

“…To facilitate extensive studies for future disease-related miRNAs research, we developed a freely available web server called HGCNELMDA is available at http://124.221.62.44:8080/HGCNELMDA.jsp .…”
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Rancang Bangun Aplikasi Presensi Guru Sekolah Menggunakan Sidik Jari Dan Raspberry Pi by Afis Julianto, Danuri Danuri, Agus Tedyyana

“…Keywords: Fingerprint, Presence, Web Server, Raspberry Pi…”
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A web-based dynamic Nomogram for predicting instrumental activities of daily living disability in older adults: a nationally representative survey in China by Li Zhang, Huijie Cui, Qiuzhi Chen, Yan Li, Chunxia Yang, Yanfang Yang

“…The internal and external calibration plots for predictions of IADL disability were in excellent agreement. An online web server was built ( https://lilizhang.shinyapps.io/DynNomapp/ ) to facilitate the use of the nomogram. …”
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MSCAN: multi-scale self- and cross-attention network for RNA methylation site prediction by Honglei Wang, Tao Huang, Dong Wang, Wenliang Zeng, Yanjing Sun, Lin Zhang

“…Furthermore, MSCAN reveals a strong association among different types of RNA modifications from an experimental perspective. A user-friendly web server for predicting twelve widely occurring human RNA modification sites (m6A, m1A, m5C, m5U, m6Am, m7G, Ψ, I, Am, Cm, Gm, and Um) is available at http://47.242.23.141/MSCAN/index.php . …”
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TOBFAC: the database of tobacco transcription factors by Brannock Jennifer F, Laudeman Thomas W, Bokowiec Marta T, Rushton Paul J, Chen Xianfeng, Timko Michael P

“…The web interface was implemented in JavaScript and Perl CGI running on an Apache web server. The computationally intensive data processing and analysis pipelines were run on an Apple XServe cluster with more than 20 nodes.…”
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CircPCBL: Identification of Plant CircRNAs with a CNN-BiGRU-GLT Model by Pengpeng Wu, Zhenjun Nie, Zhiqiang Huang, Xiaodan Zhang

“…Ultimately, CircPCBL is available as a web server, from which the data and source code can also be downloaded free of charge.…”
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In-Silico Evaluation of the Folding and Structural Stability of Aptamers for Application in the Design of a Biosensor for Testosterone Detection by Ariadna Medina, Ana L. Torres, Aurora Antonio

“…The stability of a set of nine sequences with proven interaction with testosterone was evaluated under different conditions, specifically, folding temperature (8.0 °C, 20 °C, and 30 °C), [Na⁺] (1.0 mm M, 50 mM, and 150 mM) and [Mg²⁺] (1.0 mm M, 2.0 mM, 3.0 mM, and 4.0 mM), with the MFold web server, RNA Composer, and PyMOL. The affinity and molecular interaction assays were carried out between each of the aptamers and three analytes: testosterone, testosterone undecanoate, and androstenedione using Auto dock Vina, Chimera, PyMOL, and Discovery Studio. …”
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Tyrosinase Inhibitory Ability and In Vitro, In Vivo Acute Oral and In Silico Toxicity Evaluation of Extracts Obtained from Algerian Fir (<i>Abiesnumidica</i> de Lannoy ex CARRIERE)... by Djamila Benouchenne, Ines Bellil, Sana Hazar Tachour, Salah Akkal, Hanène Djeghim, Fethi Farouk Kebaili, Gema Nieto, Douadi Khelifi

“…The absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties were identified by the pkCSM web server. The data stated that ethyl acetate (EA) presented strong anti-tyrosinase apt. …”
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The Glossaryfication Web Service: an automated glossary creation tool to support the One Health community by Nazareno Scaccia, Taras Günther, Estibaliz Lopez de Abechuco, Matthias Filter

“…The GWS developed with the open-source desktop software KNIME Analytics Platform and runs as a web service on a KNIME Web Server infrastructure. The core data processing functionality in the GWS is based on KNIME’s Textprocessing extension. …”
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Computational prediction of nimbanal as potential antagonist of respiratory syndrome coronavirus by Aanuoluwa Eunice Adegbola, Olumide Samuel Fadahunsi, Abdulahi Alausa, Ayodeji Zabdiel Abijo, Toheeb Adewale Balogun, Taiwo Sarah Aderibigbe, Banjo Semire, Peter Ifeoluwa Adegbola

“…The physicochemical and pharmacokinetic properties of the compounds were predicted using the Swissadme web server.Twenty-two of the compounds showed inhibition potential similar to dexamethasone and remdesvir, which had binding affinity of −6.8 and −6.3 kcal/mol respectively. …”
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