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XL < sub > 1 < /sub > R-Net: Explainable AI-driven improved L < sub > 1 < /sub > -regularized deep neural architecture for NSCLC biomarker identification
CONCLUSION: A set of seven novel biomarkers that have not been reported in the literature could be investigated for their potential contribution towards NSCLC therapy. Given NSCLC's genetic diversity, using only one omics data type may not adequately capture the tumor's complexity. Multiomics data and its integration with other sources will be examined in the future to better understand NSCLC heterogeneity.PMID:38000327 | DOI:10.1016/j.compbiolchem.2023.107990 (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - November 24, 2023 Category: Bioinformatics Authors: Kountay Dwivedi Ankit Rajpal Sheetal Rajpal Virendra Kumar Manoj Agarwal Naveen Kumar Source Type: research

Named entity recognition of rice genes and phenotypes based on BiGRU neural networks
Comput Biol Chem. 2023 Nov 3;108:107977. doi: 10.1016/j.compbiolchem.2023.107977. Online ahead of print.ABSTRACTNamed Entity Recognition (NER) is a fundamental but crucial task in natural language processing (NLP) and big data analysis, with wide application range. NER for rice genes and phenotypes is a technique to identify genes and phenotypes from a large amount of text. NER for rice genes and phenotypes can facilitate the acquisition of information in the field of crops and provide references for our research on higher quality crops. At the same time, named entity recognition still faces many challenges. In this paper,...
Source: Computational Biology and Chemistry - November 23, 2023 Category: Bioinformatics Authors: Kangjie Wu Liqian Xu Xinxiang Li Youhua Zhang Zhenyu Yue Yujia Gao Yiqiong Chen Source Type: research

Computational molecular perspectives on novel carbazole derivative as an anti-cancer molecule against CDK1 of breast and colorectal cancers via gene expression studies, novel two-way docking strategies, molecular mechanics and dynamics
Comput Biol Chem. 2023 Nov 7;108:107979. doi: 10.1016/j.compbiolchem.2023.107979. Online ahead of print.ABSTRACTWith increase in cancer incidences, alternative strategies for disease management are of utmost importance. Carbazole, is a compound that is being studied extensively as an anti-cancer compound. In this work, we aimed to investigate a carbazole derivative against specific cancer types such as breast and colorectal, based on the off-target analyses of carbazole derivative. The present work shortlisted 6 proteins that have an association in both cancer types, and then employed two different molecular docking strate...
Source: Computational Biology and Chemistry - November 21, 2023 Category: Bioinformatics Authors: Eashita Suvarna Anagha S Setlur Chandrashekar K Sridharan M Vidya Niranjan Source Type: research

Netting into the Sophoretin pool: An approach to trace GSTP1 inhibitors for reversing chemoresistance
Comput Biol Chem. 2023 Nov 7;108:107981. doi: 10.1016/j.compbiolchem.2023.107981. Online ahead of print.ABSTRACTChemoresistance, a significant challenge in cancer treatment, is often associated with the cellular glutathione-related detoxification system. The GSTP1 isoenzyme (glutathione S-transferases) plays a critical role in the cytoplasmic inactivation of anticancer drugs. This suggests the identification of GSTP1 inhibitors to combat chemoresistance. We screened Sophoretin (also called quercetin) derivatives for molecular properties, pharmacokinetics, and toxicity profiles. Following that, we conducted molecular dockin...
Source: Computational Biology and Chemistry - November 17, 2023 Category: Bioinformatics Authors: Kunal Bhattacharya Shikha Mahato Satyendra Deka Nongmaithem Randhoni Chanu Amit Kumar Shrivastava Pukar Khanal Source Type: research

Revisiting structural organization of proteins at high temperature from a network perspective
Comput Biol Chem. 2023 Nov 3;108:107978. doi: 10.1016/j.compbiolchem.2023.107978. Online ahead of print.ABSTRACTInteractions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins ...
Source: Computational Biology and Chemistry - November 13, 2023 Category: Bioinformatics Authors: Suman Hait Sudip Kundu Source Type: research

Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods
This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl rin...
Source: Computational Biology and Chemistry - November 13, 2023 Category: Bioinformatics Authors: Manwi Shankar Majji Sai Sudha Rani Priyanka Gopi Arsha P Prateek Pandya Source Type: research