Identification of Viral Taxon-Specific Genes (VTSG): Application to by Shinduck Kang, Young-Chang Kim

“…First, based on the dogma “protein structure determines its function,” we hypothesized that the specific sequence can be identified by the specific structure. …”
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Molecular Modeling and Simulation Analysis of Antimicrobial Photodynamic Therapy Potential for Control of COVID-19 by Maryam Pourhajibagher

“…In this in silico study, SARS-CoV-2-SG was selected as a novel target for curcumin as a photosensitizer during aPDT to exploit its physicochemical properties, molecular modeling, hierarchical nature of protein structure, and functional analysis using several bioinformatics tools and biological databases. …”
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Expression and Characterization of the Novel Gene fr47 during Freezing in the Wood Frog, Rana sylvatica by Katrina J. Sullivan, Kyle K. Biggar, Kenneth B. Storey

“…De novo analysis of FR47 protein structure revealed a likelihood of membrane associated function and possible GRB2 association. …”
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Conformational Dynamics of Mitochondrial Inorganic Pyrophosphatase hPPA2 and Its Changes Caused by Pathogenic Mutations by Ekaterina Bezpalaya, Svetlana Kurilova, Nataliya Vorobyeva, Elena Rodina

“…The results of this work allow for deeper insight into the structural basis of PPase function and the possible effects of pathogenic mutations on the protein structure and function.…”
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In Silico Analysis on the Interaction of Haloacid Dehalogenase from Bacillus cereus IndB1 with 2-Chloroalkanoic Acid Substrates by Enny Ratnaningsih, Saepulloh Saepulloh

“…This research performed computational studies to predict the Bcfd1 protein structure and analyse the interaction of Bcfd1 towards several haloacid substrates to comprehend their enantioselectivity and substrates’ range. …”
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Homology Modeling and Expression of Recombinant NS5-RdRp Based on the Indonesian Local Strain of Dengue Virus for Anti-Dengue Drug Development by Toto Subroto, Ade Rizqi Ridwan Firdaus, Shinta Kusumawardani, Taufik Ramdani Tohari, Theresia Adventina Nababan, Wulan Pertiwi, Muhammad Fadhlillah, Sri Agung Fitri Kusuma, Yaya Rukayadi

“…Future studies on the development of an anti-dengue drug model that confirms the inhibition of the binding domain in the recombinant RdRp protein structure will be required to provide more insight and expand the development of a universal anti-dengue strategy in Indonesia. …”
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Transcytosis of T4 Bacteriophage Through Intestinal Cells Enhances Its Immune Activation by Amanda Carroll-Portillo, October Barnes, Cristina N. Coffman, Cody A. Braun, Sudha B. Singh, Henry C. Lin

“…Interactions between bacteriophages with mammalian immune cells are of great interest and most phages possess at least one molecular pattern (nucleic acid, sugar residue, or protein structure) that is recognizable to the immune system through pathogen associated molecular pattern (PAMP) receptors (i.e., TLRs). …”
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Biallelic mutations in CDC20 cause female infertility due to oocyte maturation abnormality by Guangzhong Jiao, Jinhao Xing, Zhaoli Du, Hongchu Bao, Xiaoyan Liu

“…Based on the three-dimensional (3D) structures of the CDC20 protein used to assess the effect of the mutant, the mutant causes a change in hydrogen bond in the protein structure, which may affect the stability of the mutant protein. …”
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Unveiling the biological effects of radio-frequency and extremely-low frequency electromagnetic fields on the central nervous system performance by Ramin Eskandani, Mohammad Ismail Zibaii

“…Results: Exposure to RF-EMR can potentially exert adverse effects on the performance of CNS by inducing changes in the permeability of the blood-brain barrier (BBB), neurotransmitter levels, calcium channel regulation, myelin protein structure, the antioxidant defense system, and metabolic processes. …”
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Hypolipidemic Effect of Chloroform Extract of Lagenaria siceraria: Potential Inhibitory Activity of Phytochemicals Targeting the HMG-CoA Reductase Revealed by Molecular Docking and... by Qudsia Kanwal, Mahmood Ahmed, Atiq Ur-Rehman, Aneela Anwar, Samiah Shahid, Atif Shahzad, Attaullah Shah Bukhari, Muhammad Ahmad, Numan Yousaf, Muhammad Muddassar

“…Moreover, the docking results were refined by 100 ns MD simulations which revealed that stigmastan-3-ol extract formed a stable complex with protein and did not induce any conformational changes in protein structure.…”
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Human SLC26A1 Gene Variants: A Pilot Study by Paul A. Dawson, Pearl Sim, David W. Mudge, David Cowley

“…The M132 amino acid in human SAT1 is conserved with 15 other species and is located within the third transmembrane domain of the predicted SAT1 protein structure, suggesting that this amino acid may be important for SAT1 function. …”
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Leveraging Quantum LSTM for High-Accuracy Prediction of Viral Mutations by Prashanth Choppara, Bommareddy Lokesh

“…The model identifies mutation hotspots that affect virus spread, immune evasion, and protein structure, providing key biological insights for future vaccine development and therapeutic strategies.…”
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Bioinformatics Method Was Used to Analyze the Highly Expressed Gene FAM83A of Breast Cancer in Young Women by Yongzhe Tang, Hao Wang, Qi He, Yuanyuan Chen, Jie Wang

“…We performed an analysis of the gene structure, subcellular localization, physicochemical properties of the encoding products, functional sites, protein structure, and functional domains. Results. Through SAGE DGED, a total of 185 genes with expression differences were found. …”
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Antagonistic functions of CTL1 and SUH1 mediate cell wall assembly in Arabidopsis by Nguyen Thi Thuy, Hyun‐Jung Kim, Suk‐Whan Hong

“…Abstract Plant genomes contain numerous genes encoding chitinase‐like (CTL) proteins, which have a similar protein structure to chitinase belonging to the glycoside hydrolase (GH) family but lack the chitinolytic activity to cleave the β‐1,4‐glycosidic bond in chitins, polymers of N‐acetylglucosamine. …”
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Optimizing the Extraction of Keratin from Cattle Hoof Using Central Composite Design by Kelem Tiessasie Yilma, Tamrat Tesfaye, Haymanot Enawgaw, Million Ayele, Derseh Yilie Limeneh, Magdi Gibril, Fangong Kong

“…It is observed that the Biuret and Fourier-transform infrared spectroscopy (FTIR) tests showed better preservation of protein structure in extractive keratin. The FTIR spectra, indicates that amide I and amide II occur at a wave length of 1633 and 1542 cm−1 for raw cattle hoof and at wave length of 1650 and 1542 cm−1 for keratin protein, respectively. …”
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The WRKY Transcription Factor Genes in Lotus japonicus by Hui Song, Pengfei Wang, Zhibiao Nan, Xingjun Wang

“…Based on the WRKY protein structure, L. japonicus WRKY (LjWRKY) genes can be classified into three groups (I–III). …”
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XGBoost-enhanced ensemble model using discriminative hybrid features for the prediction of sumoylation sites by Salman Khan, Sumaiya Noor, Tahir Javed, Afshan Naseem, Fahad Aslam, Salman A. AlQahtani, Nijad Ahmad

“…This study introduces XGBoost-Sumo, a robust model to predict sumoylation sites by integrating protein structure and sequence data. The model utilizes a transformer-based attention mechanism to encode peptides and extract evolutionary features through the PsePSSM-DWT approach. …”
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Determination of damaging SNP’s in SHANK3 gene with in silico methods by İrem Gülfem Albayrak, Şeyma Yektar, Süeda Kaya

“…In the presented research, effects on protein structure of this SNPs are discussed. Conclusions This in silico study improves our understanding of the complicated molecular changes associated with the SHANK3 gene and contributes to a more comprehensive understanding of the genetic landscape. …”
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Novel Pathogenic Variant in TGFBR2 Confirmed by Molecular Modeling Is a Rare Cause of Loeys-Dietz Syndrome by Michael T. Zimmermann, Raul A. Urrutia, Patrick R. Blackburn, Margot A. Cousin, Nicole J. Boczek, Eric W. Klee, Colleen Macmurdo, Paldeep S. Atwal

“…Molecular modeling reveals alteration of local protein structure as a result of this pathogenic variant. …”
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SNP Analysis of the SOD1 gene involved in Amyotrophic Lateral Sclerosis (ALS) by Hetal Patel, Anandita Banerjee, Pritha Saha, Subramaniyan Divya, Palaniyandi Ravanan, Priti Talwar

“…The variants with most pathogenicity and clinical significance were further analyzed for stability and found to destabilize the protein structure based on Gibbs Free Energy (ddG) values. …”
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