Klinakis, Apostolos Cournia, Zoe Rampias, Theodoros
Published in
Computational and Structural Biotechnology Journal
During the past two years, the world has been ravaged by a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Acquired mutations in the SARS-CoV-2 genome affecting virus infectivity and/or immunogenicity have led to a number of novel strains with higher transmissibility compared to the original Wuhan strain....
Liu, Qing Wang, Yuwei Leung, Elaine Lai-Han Yao, Xiaojun
Published in
Computational and Structural Biotechnology Journal
The key step for SARS-CoV-2 to infect human cells is the membrane fusion triggered by the binding of the viral extracellular Spike protein to the human extracellular receptor, the angiotensin-converting enzyme 2 (ACE2). Although the Cryo-electron microscopy (Cryo-EM) uncovered the static atomic details of ACE2 homodimers, there is still a lack of r...
Zahra, Shafaque Singh, Ajeet Poddar, Nikita Kumar, Shailesh
Published in
Computational and Structural Biotechnology Journal
The emergence of distinct classes of non-coding RNAs has led to better insights into the eukaryotic gene regulatory networks. Amongst them, the existence of transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs) demands exploration in the plant kingdom. We have designed a methodology to uncover the entire perspective of tncRNAome in plants. Using th...
Wu, Yifei Pegan, Scott D. Crich, David Desrochers, Ellison Starling, Edward B. Hansen, Madelyn C. Booth, Carson Nicole Mullininx, Lauren Lou, Lei Chang, Kuan Y.
...
Published in
Computational and Structural Biotechnology Journal
Although scientists around the world have put lots of effort into the development of new treatments for COVID-19 since the outbreak, no drugs except Veklury (remdesivir) have been approved by FDA. There is an urgent need to discover some alternative antiviral treatment for COVID-19. Because polyphenols have been shown to possess antiviral activitie...
Omranian, Sara Angeleska, Angela Nikoloski, Zoran
Published in
Computational and Structural Biotechnology Journal
Identification of protein complexes from protein-protein interaction (PPI) networks is a key problem in PPI mining, solved by parameter-dependent approaches that suffer from small recall rates. Here we introduce GCC-v, a family of efficient, parameter-free algorithms to accurately predict protein complexes using the (weighted) clustering coefficien...
Jiang, Leiming Chen, Qiuyang Bei, Mingrong Shao, Mengting Xu, Jianzhen
Published in
Computational and Structural Biotechnology Journal
The interactions among non-coding RNA (ncRNA) and RNA binding protein (RBP) are increasingly recognized as one of basic mechanisms in gene regulation, and play a crucial role in cancer progressions. However, the current understanding of this regulation network, especially its dynamic spectrum according to the differentially expressed nodes ( i.e. n...
Khazen, Georges Gyulkhandanian, Aram Issa, Tina Maroun, Rachid C.
Published in
Computational and Structural Biotechnology Journal
Because of their considerable number and diversity, membrane proteins and their macromolecular complexes represent the functional units of cells. Their quaternary structure may be stabilized by interactions between the α-helices of different proteins in the hydrophobic region of the cell membrane. Membrane proteins equally represent potential pharm...
Stehantsev, Pavlo Stetsenko, Artem Nemchinova, Mariia Aduri, Nanda Gowtham Marrink, Siewert J. Gati, Cornelius Guskov, Albert
Published in
Computational and Structural Biotechnology Journal
The ASCT1 transporter of the SLC1 family is largely involved in equilibration of neutral amino acids’ pools across the plasma membrane and plays a prominent role in the transport of both L- and D-isomers of serine, essential for the normal functioning of the central nervous system in mammals. A number of mutations in ASCT1 (E256K, G381R, R457W) hav...
Schwab, Julian D. Ikonomi, Nensi Werle, Silke D. Weidner, Felix M. Geiger, Hartmut Kestler, Hans A.
Published in
Computational and Structural Biotechnology Journal
Regulatory dependencies in molecular networks are the basis of dynamic behaviors affecting the phenotypical landscape. With the advance of high throughput technologies, the detail of omics data has arrived at the single-cell level. Nevertheless, new strategies are required to reconstruct regulatory networks based on populations of single-cell data....
Zamith-Miranda, Daniel Amatuzzi, Rafaela F. Munhoz da Rocha, Isadora F. Martins, Sharon T. Lucena, Aline C.R. Vieira, Alexandre Z. Trentin, Gabriel Almeida, Fausto Rodrigues, Marcio L. Nakayasu, Ernesto S.
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Published in
Computational and Structural Biotechnology Journal
Candida auris has emerged as a serious worldwide threat by causing opportunistic infections that are frequently resistant to one or more conventional antifungal medications resulting in high mortality rates. Against this backdrop, health warnings around the world have focused efforts on understanding C. auris fungal biology and effective prevention...
