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Journal articles on the topic 'Structural bio-Informatics'

Author: Grafiati

Published: 8 June 2024

Last updated: 31 July 2025

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1

Kousar, Begum* Zarafsha Abbas Nukala Umasri K. Mounika. "ADVANCED COMPUTATIONAL STRUCTURAL INFORMATICS BY STEREOLITHOGRAPHY – A 3D PRINTING." INDO AMERICAN JOURNAL OF PHARMACEUTICAL SCIENCES 05, no. 01 (2018): 492–501. https://doi.org/10.5281/zenodo.1161659.

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Computational Structural Informatics is the discipline of science which investigates the structure and properties of scientific information, as well as the regularities and scientific information activity, its theory, history, methodology and organisation. The use of computers in solving information problems in the life sciences, mainly, it involves the creation of extensive electronic databases on structural informatics like 2D printing etc. Secondarily, it involves techniques such as the three-dimensional modelling of biomolecules and biologic systems. It is also used largely for the identif

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Et. al., Ravi Kumar A,. "A Review on Design and Development of Performance Evaluation Model for Bio-Informatics Data Using Hadoop." Turkish Journal of Computer and Mathematics Education (TURCOMAT) 12, no. 2 (2021): 1546–63. http://dx.doi.org/10.17762/turcomat.v12i2.1432.

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The paper reviews the usage of the platform Hadoop in applications for systemic bioinformatics. Hadoop offers another system for Structural Bioinformatics to break down broad fractions of the Protein Data Bank that is crucial to high-throughput investigations of (for example) protein-ligand docking, protein-ligand complex clustering, and structural alignment. In specific, we review different applications of high-throughput analyses and their scalability in the literature using Hadoop. In comparison to revising the algorithms, we find that these organisations typically use a realized executable

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Lakhrissi, Younes, Mohamed Rbaa, Burak Tuzun, et al. "Synthesis, structural confirmation, antibacterial properties and bio-informatics computational analyses of new pyrrole based on 8-hydroxyquinoline." Journal of Molecular Structure 1259 (July 2022): 132683. http://dx.doi.org/10.1016/j.molstruc.2022.132683.

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4

Shimizu, Nobutaka, Shinya Saijyo, Hiromasa Ota, et al. "3P015 Bio-SAXS in the Platform for Drug Discovery, Informatics, and Structural Life Science (PDIS)(01A. Protein: Structure,Poster)." Seibutsu Butsuri 53, supplement1-2 (2013): S214. http://dx.doi.org/10.2142/biophys.53.s214_3.

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5

Rahman, Monzilur, and Md Masud Parvege. "In silico structural analysis of Hantaan virus glycoprotein G2 and conserved epitope prediction for vaccine development." Journal of Applied Virology 3, no. 3 (2014): 62. http://dx.doi.org/10.21092/jav.v3i3.38.

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<p>Hantaan virus (HNTV) is an etiological agent of potentially fatal hemorrhagic fever with renal syndrome (HFRS). The virus infects a large number of patients annually with a mortality rate more than 10%. However, no treatment option or vaccine is available against the virus. Between two envelope proteins, HNTV glycoprotein G2 has higher antigenicity making it a better target for vaccine development. However, 3-D structure of the protein is not available which is important for identifying epitopes that are essential for vaccine design. Therefore, this study was designed to predict a str

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George Priya Doss, C., C. Sudandiradoss, R. Rajasekaran, Rituraj Purohit, K. Ramanathan, and Rao Sethumadhavan. "Identification and structural comparison of deleterious mutations in nsSNPs of ABL1 gene in chronic myeloid leukemia: A bio-informatics study." Journal of Biomedical Informatics 41, no. 4 (2008): 607–12. http://dx.doi.org/10.1016/j.jbi.2007.12.004.

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7

Kumar, Archana, T. B. Sridharn, and Kamini A. Rao. "Role of Seminal Plasma Proteins in Effective Zygote Formation- A Success Road to Pregnancy." Protein & Peptide Letters 26, no. 4 (2019): 238–50. http://dx.doi.org/10.2174/0929866526666190208112152.

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Seminal plasma proteins contributed by secretions of accessory glands plays a copious role in fertilization. Their role is overlooked for decades and even now, as Artificial Reproduction Techniques (ART) excludes the plasma components in the procedures. Recent evidences suggest the importance of these proteins starting from imparting fertility status to men, fertilization and till successful implantation of the conceptus in the female uterus. Seminal plasma is rich in diverse proteins, but a major part of the seminal plasma is constituted by very lesser number of proteins. This makes isolation

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Gheraibia, Youcef, Abdelouahab Moussaoui, Youcef Djenouri, Sohag Kabir, Peng-Yeng Yin, and Smaine Mazouzi. "Penguin Search Optimisation Algorithm for Finding Optimal Spaced Seeds." International Journal of Software Science and Computational Intelligence 7, no. 2 (2015): 85–99. http://dx.doi.org/10.4018/ijssci.2015040105.

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This paper develops PeSeeD, a new metaheuristic algorithm for finding optimal spaced seed. Sequences matching is a hot topic in bio-informatics, which is used in many applications such as understanding the functional, structural, or evolutionary relationships between the sequences. The most relevant sequences matching methods are based on seeds designed to match two biological sequences. The first approach which introduced seeds was facilitated via Blastn tool, the approach builds seeds of 11 length size. However, it is clear that not all local alignments have to include an identical fragment

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Javed, Ambreen, Gulshan Ara Trali, Hassan Burair Abbas, and Alia Sadiq. "IN SILICO CHARACTERIZATION OF HUMAN INTERFERON ALPHA/BETA RECEPTOR 2 (ISOFORM A, B AND C) PROTEIN." PAFMJ 71, no. 6 (2021): 2091–94. http://dx.doi.org/10.51253/pafmj.v71i6.6571.

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Objective: To predict the tertiary structure of human interferon alpha/beta receptor 2 protein. Study Design: Structure prediction by using bio informatics tools. Place and Duration of Study: Department of Biochemistry, Swat Medical College (STMC), Saidu Shareef, Swat, Pakistan, from Aug 2019 to Dec 2019. Methodology: All protein sequences of human interferon alpha/beta receptor 2 (isoforma, b and c) (IFNAR-2) were retrieved through the BLAST search (The Basic Local Alignment Search Tool) from available databases ‘NCBI’ (National Centre for Biotechnology Information) and ‘Uni

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10

Lakhrissi, Younes, Mohamed Rbaa, Burak Tuzun, et al. "Corrigendum to ‘Synthesis, Structural confirmation, Antibacterial Properties and Bio-Informatics Computational Analyses of New Pyrrole Based on 8-Hydroxyquinoline’ Journal of Molecular Structure 1259 (2022) 132683." Journal of Molecular Structure 1280 (May 2023): 134988. http://dx.doi.org/10.1016/j.molstruc.2023.134988.

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11

Nadeem, Muhammad, Sibtain Ahmad, Rizwan Shaukat, Masood Ashiq, and Arslan Akram. "Genome wide analysis of growth and development genes in cattle (<i>Bos taurus</i>) and Buffalo (<i>Bubalus bubalis</i>)." Ricos Biology 3, no. 1 (2025): 57–79. https://doi.org/10.33687/ricosbiol.03.01.0033.

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Bos taurus and Bubalus bubalis have been major source of meat since about 10000 years. 50 genes associated with growth and development in Bos taurus and Bublus bubalis were analyzed integratedly by GWAS performing chromosomal mapping, gene structure, conserved motif analysis, gene expression, GO annotation analysis, protein-protein association and phylogenetic analysis, Main bio-informatics tools used were NCBI, Expasy, WebScipio, iTOL , heatmapper, string and MEGA 5. GH, TG and NEB were found as major genes of beef production by visulising expression by heatmapper, motif analysis by MEME and

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Khuntia, Bharat Krushna, Vandna Sharma, Sahar Qazi, et al. "Ayurvedic Medicinal Plants Against COVID-19: An In Silico Analysis." Natural Product Communications 16, no. 11 (2021): 1934578X2110567. http://dx.doi.org/10.1177/1934578x211056753.

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Even after one and a half years since the outbreak of COVID-19, its complete and effective control is still far from being achieved despite vaccination drives, symptomatic management with available drugs, and wider lockdowns. This has inspired researchers to screen potential phytochemicals from medicinal plants against SARS-CoV-2, adopting a bio-informatics approach. The current study aimed to assess anti-viral activity of the phytochemicals derived from Ayurvedic medicinal plants against SARS-CoV-2 drug targets [3-chymotrypsin-like protease (3CLpro) and RNA dependent RNA polymerase (RdRp)] us

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Kara, Yeliz, Yeşim Saǧlam Özkan, Asad Ullah, Yasser Salah Hamed, and Melaku Berhe Belay. "QSPR modeling of some COVID-19 drugs using neighborhood eccentricity-based topological indices: A comparative analysis." PLOS One 20, no. 5 (2025): e0321359. https://doi.org/10.1371/journal.pone.0321359.

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COVID-19, which emerged in 2019, is a disease caused by a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARSCoV-2), and has caused a worldwide epidemic. During and after this outbreak, it has been confirmed once again that finding a drug to prevent and end such diseases as soon as possible is an important issue. However, drug discovery and to determine a molecule’s physical characteristics in a lab takes effort and time and is a costly process. Relevant information about molecules can be obtained by calculating topological indices, which are molecular descriptive numerical

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Chacko, Anita, Shankarrao Patil, Atul Upadhayay, et al. "A High Throughput Exome Sequencing Approach To Analyse Events Within a Good Responder CML Patient Under Imatinib At Diagnosis and Under Remission." Blood 122, no. 21 (2013): 5161. http://dx.doi.org/10.1182/blood.v122.21.5161.5161.

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Abstract Background Genome sequencing has emerged recently as a technology that can be used to address questions regarding the clonal evolution of cancers. This has the potential to be translated into practical applications in a clinical setting. We have undertaken a case study by carrying out whole exome sequencing of a patient with CML since its clinical outcome varies amongst patients during the progression of disease. Our study is an attempt for a better understanding of why patients differ in their response to different dose of drug regimen and to determine its role in clinical outcome. O

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15

Halim, Sobia Ahsan, Almas Gul Sikandari, Ajmal Khan та ін. "Structure-Based Virtual Screening of Tumor Necrosis Factor-α Inhibitors by Cheminformatics Approaches and Bio-Molecular Simulation". Biomolecules 11, № 2 (2021): 329. http://dx.doi.org/10.3390/biom11020329.

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Tumor necrosis factor-α (TNF-α) is a drug target in rheumatoid arthritis and several other auto-immune disorders. TNF-α binds with TNF receptors (TNFR), located on the surface of several immunological cells to exert its effect. Hence, the use of inhibitors that can hinder the complex formation of TNF-α/TNFR can be of medicinal significance. In this study, multiple chem-informatics approaches, including descriptor-based screening, 2D-similarity searching, and pharmacophore modelling were applied to screen new TNF-α inhibitors. Subsequently, multiple-docking protocols were used, and four-fold po

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16

Lee, Cherl-Joon, Wonseok Shin, Minsik Song, et al. "Comparison of digital PCR platforms using the molecular marker." Genomics & Informatics 21, no. 2 (2023): e24. http://dx.doi.org/10.5808/gi.23008.

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Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation P

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17

Muhammed, Amanat, F. M. Shahid Ud Daula A, and Islam Fakhrul. "Potential usage of Zerumbone to suppress inflammation: An in silico study." American Journal of Science and Medical Research 8, no. 2 (2022): 1–11. https://doi.org/10.5281/zenodo.7215994.

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<strong>ABSTRACT</strong> A significant cyclic sesquiterpenoid known as Zerumbone was extracted from <em>Zingiber roseum</em> using the volume liquid chromatographic (VLC) technique. It’s a naturally occurring phytochemical having a variety of physiological properties, including antioxidant, anti-ulcer, and antiproliferative action. This study's major goal was to evaluate Zerumbone's anti-inflammatory effectiveness against the inflammation receptors-Secretory Phospholipase A2 (sPLA2), Cyclooxygenase-2 (COX-2), Tumor Necrosis Factor (TNF-alpha), and Inducible Nitric Oxide Synthase

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18

Luu, Rachel K., and Markus J. Buehler. "Materials Informatics tools in the context of bio-inspired material mechanics." Journal of Applied Mechanics, April 12, 2023, 1–17. http://dx.doi.org/10.1115/1.4062310.

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Abstract The analysis and design of materials is often a slow process that may take weeks, months, or years. And, many current material platforms rely on expensive raw material sources and fail to achieve sustainability goals. Meanwhile, bio-inspired Materials Informatics – fueled by emerging techniques such as multiscale modeling, machine learning and autonomous experimentation – is transforming the way materials are understood, discovered, developed, and selected. The impact of these tools is particularly noteworthy since they can be used to develop materials with fewer resources and with gr

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19

Perotin, Jeanne-Marie, Myriam Polette, Gaëtan Deslée, and Valérian Dormoy. "CiliOPD: a ciliopathy-associated COPD endotype." Respiratory Research 22, no. 1 (2021). http://dx.doi.org/10.1186/s12931-021-01665-4.

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AbstractThe pathophysiology of chronic obstructive pulmonary disease (COPD) relies on airway remodelling and inflammation. Alterations of mucociliary clearance are a major hallmark of COPD caused by structural and functional cilia abnormalities. Using transcriptomic databases of whole lung tissues and isolated small airway epithelial cells (SAEC), we comparatively analysed cilia-associated and ciliopathy-associated gene signatures from a set of 495 genes in 7 datasets including 538 non-COPD and 508 COPD patients. This bio-informatics approach unveils yet undescribed cilia and ciliopathy genes

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20

"Identiﬁcation and structural comparison of deleterious mutations in nsSNPs of IL-6 gene in inflammation: A bio-informatics study". Inflammation and Cell Signaling, 27 жовтня 2015. http://dx.doi.org/10.14800/ics.777.

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21

Li, Xinzhong, Peter A. Thomason, Dominic J. Withers, and James Scott. "Bio-informatics analysis of a gene co-expression module in adipose tissue containing the diet-responsive gene Nnat." BMC Systems Biology 4, no. 1 (2010). http://dx.doi.org/10.1186/1752-0509-4-175.

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22

Dash, Adyasha, Manjusha Pandey, and Siddharth Swarup Rautaray. "novel deep neural network framework for biomedical named entity recognition." International journal of health sciences, June 23, 2022, 4310–24. http://dx.doi.org/10.53730/ijhs.v6ns5.9557.

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With the dramatic improvements in the field of bio-informatics, extracting information from text and analyzing the association between the entities has received more attention in the past few years. Entity Recognition (ER) meant to extract and recognize the entities from any text. Biomedical Named Entity Recognition (BNER) gets more and more attention from the researchers since it is a fundamental task in biomedical information extraction. Various methods has been proposed to perform the task of BioNER. Different kind of approaches are dictionary based, rule based approaches, traditional machi

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23

Hussein, Baydaa Abed, Isaac Karimi, and Namdar Yousofvand. "Chemo- and bio-informatics insight into anti-cholinesterase potentials of berries and leaves of Myrtus communis L., Myrtaceae: an in vitro/in silico study." BMC Complementary Medicine and Therapies 23, no. 1 (2023). http://dx.doi.org/10.1186/s12906-023-04241-z.

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Abstract Background Myrtus communis L. (MC) has been used in Mesopotamian medicine. Here, the cholinesterase (ChE) inhibitory potential of its methyl alcohol extracts has been investigated and computationally dissected. Method The ChE inhibition has been measured based on usual Ellman’s colorimetric method compared to a canonical ChE inhibitor, eserine. Through a deep text mining, the structures of phytocompounds (= ligands) of MC were curated from ChemSpider, PubChem, and ZINC databases and docked into protein targets, AChE (PDB 1EVE) and BChE (PDB 1P0I) after initial in silico preparedness a

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Xie, Yixiao, Wen Liu, Ping Li, et al. "Soil bacterial community structure at different plant maturity stages in an annual grass–legume production system." Frontiers in Sustainable Food Systems 7 (April 18, 2023). http://dx.doi.org/10.3389/fsufs.2023.1145488.

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IntroductionTo infer changes in soil function and thus determine appropriate agronomic management practices, this study evaluated the effects of plant maturity stage on root characteristics, soil chemical and enzymatic properties, and soil bacterial community composition in an annual grass–legume production system.MethodsAnnual ryegrass or rye was sown in combination with one of three legume species at a legume ratio of 50%. Eighteen plots (six plant combinations, three replicates per combination, 20 m × 25 m plots) were tilled to a depth of 20 cm after mowing. Soil samples from each plot were

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Maryam, Jehangir1 and Syed Farhan Ahmad. "STRUCTURAL STUDIES OF ASPARTIC ENDOPEPTIDASE pep2 FROM NEOSARTORYA FISHERICA USING HOMOLGY MODELING TECHNIQUE." March 29, 2013. https://doi.org/10.5281/zenodo.1406897.

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International Journal on Bioinformatics & Biosciences (IJBB) Vol.3, No.1, March 2013 DOI : 10.5121/ijbb.2013.3102 7 STRUCTURAL STUDIES OF ASPARTIC ENDOPEPTIDASE pep2 FROM NEOSARTORYA FISHERICA USING HOMOLGY MODELING TECHNIQUES Maryam Jehangir1 and Syed Farhan Ahmad2 1Department of Bio-informatics, Shaheed Benazir Bhutto Women University, Canal Road university town, Peshawar maryam.bioinfo@yahoo.com 2Department of Biotechnology & Bioinformatics, Islamic International University, Islamabad zaid_khan68@yahoo.com ABSTRACT Aspartic endo peptidase pep2 protein of neosartorya fisherica belong

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Qatawneh. "EFFICIENT PREDICTION OF DNA-BINDING PROTEINS USING MACHINE LEARNING." June 29, 2012. https://doi.org/10.5121/ijbb.2012.2201.

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International Journal on Bioinformatics & Biosciences (IJBB) Vol.2, No.2, June 2012 DOI : 10.5121/ijbb.2012.2201 1 EFFICIENT PREDICTION OF DNA-BINDING PROTEINS USING MACHINE LEARNING S. Qatawneh1 , A. Alneaimi1 , Th. Rawashdeh1 , M. Muhairat1 , R. Qahwaji2 and S. Ipson2 1Department of Software Engineering, Faculty of Science and Information Technology, Al-Zaytoonah University of Jordan, Amman, Jordan S.Qatawneh@zuj.edu.jo 2 Informatics Research Institute, School of Computing, Informatics & Media, University of Bradford, Richmond Road, Bradford, West Yorkshire, BD7 1DP, UK S.S.Ipson@Bra

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