Kaptan, Shreyas Girych, Mykhailo Enkavi, Giray Kulig, Waldemar Sharma, Vivek Vuorio, Joni Rog, Tomasz Vattulainen, Ilpo
Published in
Computational and Structural Biotechnology Journal
SARS-CoV-2 main protease (Mpro) involved in COVID-19 is required for maturation of the virus and infection of host cells. The key question is how to block the activity of Mpro. By combining atomistic simulations with machine learning, we found that the enzyme regulates its own activity by a collective allosteric mechanism that involves dimerization...
Ramarao-Milne, Priya Jain, Yatish Sng, Letitia M.F. Hosking, Brendan Lee, Carol Bayat, Arash Kuiper, Michael Wilson, Laurence O.W. Twine, Natalie A. Bauer, Denis C.
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Published in
Computational and Structural Biotechnology Journal
New SARS-CoV-2 variants emerge as part of the virus’ adaptation to the human host. The Health Organizations are monitoring newly emerging variants with suspected impact on disease or vaccination efficacy as Variants Being Monitored (VBM), like Delta and Omicron. Genetic changes (SNVs) compared to the Wuhan variant characterize VBMs with current emp...
Kong, Weikaixin Midena, Gianmarco Chen, Yingjia Athanasiadis, Paschalis Wang, Tianduanyi Rousu, Juho He, Liye Aittokallio, Tero
Published in
Computational and Structural Biotechnology Journal
Synergistic effects between drugs are rare and highly context-dependent and patient-specific. Hence, there is a need to develop novel approaches to stratify patients for optimal therapy regimens, especially in the context of personalized design of combinatorial treatments. Computational methods enable systematic in-silico screening of combination e...
Li, Xiaoqi Lee, Lindsay Abnousi, Armen Yu, Miao Liu, Weifang Huang, Le Li, Yun Hu, Ming
Published in
Computational and Structural Biotechnology Journal
Single cell Hi-C (scHi-C) technologies enable the study of chromatin spatial organization directly from complex tissues at single cell resolution. However, the identification of chromatin loops from single cells is challenging, largely due to the extremely sparse data. Our recently developed SnapHiC pipeline provides the first tool to map chromatin...
Mulero Hernández, Juan Fernández-Breis, Jesualdo Tomás
Published in
Computational and Structural Biotechnology Journal
The process of gene regulation extends as a network in which both genetic sequences and proteins are involved. The levels of regulation and the mechanisms involved are multiple. Transcription is the main control mechanism for most genes, being the downstream steps responsible for refining the transcription patterns. In turn, gene transcription is m...
Sui, Laijian Sanders, Andrew Jiang, Wen G. Ye, Lin
Published in
Computational and Structural Biotechnology Journal
Background Bone metastasis is the most common metastatic destination in advanced breast cancer, presenting a poor prognosis and clinical challenges in management. To date, the mechanism of bone metastasis in breast cancer remains largely unclear. Methods Differentially expressed genes in primary tumours that developed bone metastases were systemati...
Selinger, Martin Věchtová, Pavlína Tykalová, Hana Ošlejšková, Petra Rumlová, Michaela Štěrba, Ján Grubhoffer, Libor
Published in
Computational and Structural Biotechnology Journal
Tick-borne encephalitis virus (TBEV), the most medically relevant tick-transmitted flavivirus in Eurasia, targets the host central nervous system and frequently causes severe encephalitis. The severity of TBEV-induced neuropathogenesis is highly cell-type specific and the exact mechanism responsible for such differences has not been fully described...
Nutho, Bodee Wilasluck, Patcharin Deetanya, Peerapon Wangkanont, Kittikhun Arsakhant, Patcharee Saeeng, Rungnapha Rungrotmongkol, Thanyada
Published in
Computational and Structural Biotechnology Journal
A global crisis of coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has impacted millions of people’s lives throughout the world. In parallel to vaccine development, identifying potential antiviral agents against SARS-CoV-2 has become an urgent need to combat COVID-19. One of the mo...
Quan, Cheng Lu, Hao Lu, Yiming Zhou, Gangqiao
Published in
Computational and Structural Biotechnology Journal
Population-scale studies of structural variation (SV) are growing rapidly worldwide with the development of long-read sequencing technology, yielding a considerable number of novel SVs and complete gap-closed genome assemblies. Herein, we highlight recent studies using a hybrid sequencing strategy and present the challenges toward large-scale genot...
Dai, Xiaoting Zhu, Xuan Bao, Lisui Chen, Xiaomei Miao, Yan Li, Yangping Li, Yuli Lv, Jia Zhang, Lingling Huang, Xiaoting
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Published in
Computational and Structural Biotechnology Journal
Secretome is involved in almost all physiological, developmental, and pathological processes, but to date there is still a lack of highly-efficient research strategy to comprehensively study the secretome of invertebrates. Adhesive secretion is a ubiquitous and essential physiological process in aquatic invertebrates with complicated protein compon...
