60 results for “Secondary Structure”

Set a search alert

Research ArticleOpen accessPhrase in the titleProtein Secondary Structure Prediction using Hybrid Recurrent Neural NetworksRomana Rahman Ema, Akhi Khatun, Md. Alam Hossain et al.The most important and challenging problem in bioinformatics is protein secondary structure prediction. The molecules of all protein organisms have three-dimensional (primary, secondary, 3-D) structures which are completely recognized by the sequence of amino acids. Protein secondary structure attributes to the polypeptide backbone of the local configuration of proteins. Most generally, the second-level prediction is indicated such as: If there … …Journal of Computer Science, Vol. 18, Issue 7 · 14 Jul 2022 · 7,332 accessesView PDF Cite

Research ArticleOpen accessPhrase in the titleLow-Homology Protein Structural Class Prediction from Secondary Structure Based on Visibility and Horizontal Visibility NetworkZhi-Qin Zhao, Liang Luo, Xiao-Yan LiuIn this study, based on the predicted secondary structures of proteins, we propose a new approach to predict protein structural classes (α,β,α/β,α+β) for three widely used low-homology data sets. Fist, we obtain two time siries from the chaos game representation of each predicted secondary structure; second, based on two time series, we construct visibility and horizontal visibility network, respectively and … …American Journal of Biochemistry and Biotechnology, Vol. 14, Issue 1 · 12 Mar 2018 · 9,668 accessesView PDF Cite

Research ArticleOpen accessPhrase in the titleImproving Protein 3D Structure Prediction Accuracy using Dense Regions Areas of Secondary Structures in the Contact MapAmer F. Al-Badarneh, Mohammad A. Khalil, Mo'taz A. Al-HamiProblem Statement: The protein folding problem is a fundamental problem in structural molecular biology. This problem describes how a protein is transformed from its primary sequence (i.e., amino acid sequence) into the three dimensional structure (3D structure) for this sequence that determines the function of the protein. The 3D structure of a protein can be represented using a square symmetrical … …American Journal of Biochemistry and Biotechnology, Vol. 4, Issue 4 · 31 Dec 2008 · 7,533 accessesView PDF Cite

Research ArticleOpen accessPhrase in the titleMinimum Free Energy Based Evaluation of mRNAs Secondary Structures Constructed by 18 Clinically Significant Exonic Single Nucleotide Polymorphisms (SNPs) and Haplotypes of 5 Missense SNPs of RB1 GeneSarder Nasir Uddin, Apurba Majumder, Khandker Khaldun Islam et al.Clinically significant 18 Single Nucleotide Polymorphisms (SNPs) from exon regions of Retinoblastoma gene (RB1) were analyzed to find out the structural variations in mRNAs. Online bioinformatic tools i.e., Vienna RNA, RNAfold were used for secondary structure analysis of mRNAs. Predicted minimum Free Energy Change (MFE) was calculated for mRNAs structures. It has been observed that the average of predicted MFE … …American Journal of Biochemistry and Biotechnology, Vol. 11, Issue 4 · 21 Oct 2015 · 8,556 accessesView PDF Cite

Research ArticleOpen accessIn the keywordsComparative Analysis of Proteins in Two Typical Chinese Thin-Shell WalnutsXu Meng, Tian YilingThis study compared functional properties and molecular characteristics of proteins from two thin-shelled walnut (Juglans regia L.) cultivars predominantly grown in China: Wen 185 and Lvling. Wen 185 walnut protein demonstrated significantly superior performance compared to Lvling across multiple functional parameters, including solubility, emulsifying capacity, foaming capacity, water absorption, and oil absorption. Molecular weight distribution analysis revealed that both proteins … …American Journal of Biochemistry and Biotechnology, Vol. 21, Issue 4 · 15 Feb 2026 · 1,481 accessesView PDF Cite

Review ArticleOpen accessIn the keywordsProtein Sequences Features Extraction for Predicting Beta- Turns and their Types: A ReviewMurtada Khalafallah Elbashir ElfakiBeta-turns are considered to be important secondary structure types that have essential role in molecular recognition, protein folding and stability. They represent 25% of protein structures, therefore they are the most common type of non-repetitive or tight turns structures. Their prediction is considered to be an important issue in bioinformatics and molecular biology, because it provides valuable information and inputs … …Journal of Computer Science, Vol. 15, Issue 9 · 1 Oct 2019 · 7,694 accessesView PDF Cite

Research ArticleOpen accessIn the keywordsBinding Studies of Natural Product Berberine with DNA G-QuadruplexNagendra K. Sharma, Pooja Lunawat, Manjusha DixitProblem statement: The ends of chromosome had highly repetitive short G and C-rich sequences of DNA. These sequences were known to form stable tetraplex type of secondary structures which help to maintain gene integratity after cell divison. Approach: Any reagent which controls the random cell division would be useful to design anticancer drugs. Therefore a many natural and synthesized molecules … …American Journal of Biochemistry and Biotechnology, Vol. 7, Issue 3 · 22 Sep 2011 · 8,797 accessesView PDF Cite

Research ArticleOpen accessIn the keywordsA Survey of Compute Intensive Algorithms for Ribo Nucleic Acids Structural DetectionRa’ed Al-Khatib, Rosni Abdullah, Nur’Aini Abdul RashidProblem statement: Finding an accurate RNA structural alignment from primary sequence due to it is time consuming and computationally NP-hard problem is a major bioinformatics challenge. According to our investigation majority of current researches were concerned on achieving faster execution time, improving space complexity and better cache management. Recently one research introduced cache-efficient Chip Multiprocessor (CMP) algorithms with good speed-up … …Journal of Computer Science, Vol. 5, Issue 10 · 31 Oct 2009 · 6,458 accessesView PDF Cite

Research ArticleOpen accessIn the abstractIn silico and in vitro Structural Analysis on the Interaction of Calmodulin and Calmodulin-Binding Motif of FKBP35 from Plasmodium knowlesiSazlinawatie Aladin, Cahyo Budiman et al.FK506-binding protein 35 (FKBP35) is a peptidyl-prolyl cis-trans isomerase found in Plasmodium knowlesi, a zoonotic malaria parasite responsible for concerning cases of malaria infection in East Malaysia. This protein contains a segment known as the calmodulin-binding motif (Pk-CBM), which is predicted to facilitate interaction with calmodulin from P. knowlesi (Pk-CaM). Although this interaction is considered promising for future antimalarial drug … …OnLine Journal of Biological Sciences, Vol. 25, Issue 2 · 10 Mar 2025 · 4,846 accessesView PDF Cite

Research ArticleOpen accessIn the abstractAnchoring Public Health Forecasts: High-Precision Obesity Prevalence Estimation Via Hybrid Geodemographic Ensemble RegressionTrenton Ward, Isaac OsunmakindeObesity remains a major driver of chronic disease and rising healthcare costs in the United States. Yet, most existing predictive models rely on single-model classifiers and rarely incorporate spatial structure or ensemble-based regression, thereby limiting their ability to capture geodemographic variation. This study introduces a hybrid unsupervised–supervised ensemble framework that integrates K-Means spatial profiling with a Stacking Regressor to address … …Journal of Computer Science, Vol. 22, Issue 7 · 31 Jul 2026 · 632 accessesView PDF Cite