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An efficient Burrows-Wheeler transform-based aligner for short read mapping
Comput Biol Chem. 2024 Mar 5;110:108050. doi: 10.1016/j.compbiolchem.2024.108050. Online ahead of print.ABSTRACTRead mapping as the foundation of computational biology is a bottleneck task under the pressure of sequencing throughput explodes. In this work, we present an efficient Burrows-Wheeler transform-based aligner for next-generation sequencing (NGS) short read. Firstly, we propose a difference-aware classification strategy to assign specific reads to the computationally more economical search modes, and present some acceleration techniques, such as a seed pruning method based on the property of maximum coverage inter...
Source: Computational Biology and Chemistry - March 6, 2024 Category: Bioinformatics Authors: Lilu Guo Hongwei Huo Source Type: research

Design, synthesis, characterization, in vitro cytotoxic, antimicrobial, antioxidant studies, DFT, thermal and molecular docking evaluation of biocompatible Co(II) complexes of N < sub > 4 < /sub > O < sub > 4 < /sub > -macrocyclic ligands
Comput Biol Chem. 2024 Feb 22;110:108032. doi: 10.1016/j.compbiolchem.2024.108032. Online ahead of print.ABSTRACTBioactive cobalt (II) macrocyclic complexes [Co(N4O4ML1)Cl2]-[Co(N4O4ML3)Cl2] have been synthesized by using the macrocyclic ligands [N4O4ML1], [N4O4ML2], and [N4O4ML3] that have an N4O4 core. These three macrocyclic ligands were all isolated in pure form, together with their complexes. Microanalytical investigations, FT-IR NMR, Mass, magnetic moments, electronic, PXRD, TGA, and EPR spectrum studies were used to analyse their structures. For these complexes, an octahedral geometry is proposed for the metal ion. ...
Source: Computational Biology and Chemistry - March 4, 2024 Category: Bioinformatics Authors: None Subhash Manish Kumar Anita Phor Monika Gupta Ashu Chaudhary Source Type: research

Design, synthesis, characterization, in vitro cytotoxic, antimicrobial, antioxidant studies, DFT, thermal and molecular docking evaluation of biocompatible Co(II) complexes of N < sub > 4 < /sub > O < sub > 4 < /sub > -macrocyclic ligands
Comput Biol Chem. 2024 Feb 22;110:108032. doi: 10.1016/j.compbiolchem.2024.108032. Online ahead of print.ABSTRACTBioactive cobalt (II) macrocyclic complexes [Co(N4O4ML1)Cl2]-[Co(N4O4ML3)Cl2] have been synthesized by using the macrocyclic ligands [N4O4ML1], [N4O4ML2], and [N4O4ML3] that have an N4O4 core. These three macrocyclic ligands were all isolated in pure form, together with their complexes. Microanalytical investigations, FT-IR NMR, Mass, magnetic moments, electronic, PXRD, TGA, and EPR spectrum studies were used to analyse their structures. For these complexes, an octahedral geometry is proposed for the metal ion. ...
Source: Computational Biology and Chemistry - March 4, 2024 Category: Bioinformatics Authors: None Subhash Manish Kumar Anita Phor Monika Gupta Ashu Chaudhary Source Type: research

Identifying promoter and enhancer sequences by graph convolutional networks
This study proposes a graph-based semi-supervised learning model (GCN4EPI) for the enhancer-promoter classification problem. We adopt a graph convolutional network (GCN) architecture to integrate interaction information with sequence features. Nodes of the constructed graph hold word embeddings of DNA sequences while edges hold the Enhancer-Promoter Interaction (EPI) information. By means of semi-supervised learning, much less data (16%) and time are needed in model training. Comparisons on a benchmark dataset of six human cell lines show that the proposed approach outperforms the state-of-the-art methods by a large margin...
Source: Computational Biology and Chemistry - March 2, 2024 Category: Bioinformatics Authors: Samet Tenekeci Selma Tekir Source Type: research

Machine learning assisted methods for the identification of low toxicity inhibitors of Enoyl-Acyl Carrier Protein Reductase (InhA)
Comput Biol Chem. 2024 Feb 20;110:108034. doi: 10.1016/j.compbiolchem.2024.108034. Online ahead of print.ABSTRACTTuberculosis (TB) is one of the life-threatening infectious diseases with prehistoric origins and occurs in almost all habitable parts of the world. TB mainly affects the lungs, and its etiological agent is Mycobacterium tuberculosis (Mtb). In 2022, more than 10 million people were infected worldwide, and 1.3 million were children. The current study considered the in-silico and machine learning (ML) approaches to explore the potential anti-TB molecules from the SelleckChem database against Enoyl-Acyl Carrier Pro...
Source: Computational Biology and Chemistry - March 2, 2024 Category: Bioinformatics Authors: Rupesh V Chikhale Heba Taha M Abdelghani Hemchandra Deka Atul Darasing Pawar Pritee Chunarkar Patil Shovonlal Bhowmick Source Type: research

Identifying promoter and enhancer sequences by graph convolutional networks
This study proposes a graph-based semi-supervised learning model (GCN4EPI) for the enhancer-promoter classification problem. We adopt a graph convolutional network (GCN) architecture to integrate interaction information with sequence features. Nodes of the constructed graph hold word embeddings of DNA sequences while edges hold the Enhancer-Promoter Interaction (EPI) information. By means of semi-supervised learning, much less data (16%) and time are needed in model training. Comparisons on a benchmark dataset of six human cell lines show that the proposed approach outperforms the state-of-the-art methods by a large margin...
Source: Computational Biology and Chemistry - March 2, 2024 Category: Bioinformatics Authors: Samet Tenekeci Selma Tekir Source Type: research

Machine learning assisted methods for the identification of low toxicity inhibitors of Enoyl-Acyl Carrier Protein Reductase (InhA)
Comput Biol Chem. 2024 Feb 20;110:108034. doi: 10.1016/j.compbiolchem.2024.108034. Online ahead of print.ABSTRACTTuberculosis (TB) is one of the life-threatening infectious diseases with prehistoric origins and occurs in almost all habitable parts of the world. TB mainly affects the lungs, and its etiological agent is Mycobacterium tuberculosis (Mtb). In 2022, more than 10 million people were infected worldwide, and 1.3 million were children. The current study considered the in-silico and machine learning (ML) approaches to explore the potential anti-TB molecules from the SelleckChem database against Enoyl-Acyl Carrier Pro...
Source: Computational Biology and Chemistry - March 2, 2024 Category: Bioinformatics Authors: Rupesh V Chikhale Heba Taha M Abdelghani Hemchandra Deka Atul Darasing Pawar Pritee Chunarkar Patil Shovonlal Bhowmick Source Type: research

MGDHGS: Gene-bridged metabolite-disease relationships prediction via GraphSAGE and self-attention mechanism
Comput Biol Chem. 2024 Feb 28;109:108036. doi: 10.1016/j.compbiolchem.2024.108036. Online ahead of print.ABSTRACTMetabolites represent the underlying information of biological systems. Revealing the links between metabolites and diseases can facilitate the development of targeted drugs. Traditional biological experiments can be used to validate the relationships of metabolite-disease, but these methods are time-consuming and labor-intensive. In contrast, the prevailing computational methods have improved efficiency but primarily rely on the metabolite-disease interactions, overlooking the impact of other biological compone...
Source: Computational Biology and Chemistry - February 29, 2024 Category: Bioinformatics Authors: Pengli Lu Ling Li Source Type: research

MGDHGS: Gene-bridged metabolite-disease relationships prediction via GraphSAGE and self-attention mechanism
Comput Biol Chem. 2024 Feb 28;109:108036. doi: 10.1016/j.compbiolchem.2024.108036. Online ahead of print.ABSTRACTMetabolites represent the underlying information of biological systems. Revealing the links between metabolites and diseases can facilitate the development of targeted drugs. Traditional biological experiments can be used to validate the relationships of metabolite-disease, but these methods are time-consuming and labor-intensive. In contrast, the prevailing computational methods have improved efficiency but primarily rely on the metabolite-disease interactions, overlooking the impact of other biological compone...
Source: Computational Biology and Chemistry - February 29, 2024 Category: Bioinformatics Authors: Pengli Lu Ling Li Source Type: research

MGDHGS: Gene-bridged metabolite-disease relationships prediction via GraphSAGE and self-attention mechanism
Comput Biol Chem. 2024 Feb 28;109:108036. doi: 10.1016/j.compbiolchem.2024.108036. Online ahead of print.ABSTRACTMetabolites represent the underlying information of biological systems. Revealing the links between metabolites and diseases can facilitate the development of targeted drugs. Traditional biological experiments can be used to validate the relationships of metabolite-disease, but these methods are time-consuming and labor-intensive. In contrast, the prevailing computational methods have improved efficiency but primarily rely on the metabolite-disease interactions, overlooking the impact of other biological compone...
Source: Computational Biology and Chemistry - February 29, 2024 Category: Bioinformatics Authors: Pengli Lu Ling Li Source Type: research

SME-MFP: A novel spatiotemporal neural network with multiangle initialization embedding toward multifunctional peptides prediction
Comput Biol Chem. 2024 Feb 20;109:108033. doi: 10.1016/j.compbiolchem.2024.108033. Online ahead of print.ABSTRACTAs a promising alternative to conventional antibiotic drugs in the biomedical field, functional peptide has been widely used in disease treatment owing to its low toxicity, high absorption rate, and biological activity. Recently, several machine learning methods have been developed for functional peptide prediction. However, the main research heavily relies on statistical features and few consider multifunctional peptide identification. So, we propose SME-MFP, a novel predictor in the imbalanced multi-label func...
Source: Computational Biology and Chemistry - February 27, 2024 Category: Bioinformatics Authors: Jing Xu Xiaoli Ruan Jing Yang Bingqi Hu Shaobo Li Jianjun Hu Source Type: research

SME-MFP: A novel spatiotemporal neural network with multiangle initialization embedding toward multifunctional peptides prediction
Comput Biol Chem. 2024 Feb 20;109:108033. doi: 10.1016/j.compbiolchem.2024.108033. Online ahead of print.ABSTRACTAs a promising alternative to conventional antibiotic drugs in the biomedical field, functional peptide has been widely used in disease treatment owing to its low toxicity, high absorption rate, and biological activity. Recently, several machine learning methods have been developed for functional peptide prediction. However, the main research heavily relies on statistical features and few consider multifunctional peptide identification. So, we propose SME-MFP, a novel predictor in the imbalanced multi-label func...
Source: Computational Biology and Chemistry - February 27, 2024 Category: Bioinformatics Authors: Jing Xu Xiaoli Ruan Jing Yang Bingqi Hu Shaobo Li Jianjun Hu Source Type: research

Integrated study reveals mechanism of Tripterygium Wilfordii against cholangiocarcinoma based on bioinformatics approaches and molecular dynamics simulation
CONCLUSION: This study identified the therapeutic role and predicted the mechanism of TW against CHOL, where TW may combat CHOL through the regulation of metabolic conditions of the body, bile acid secretion, xenobiotics metabolism, and the inflammatory response. Celastrol, triptonide, triptolide and wilforlide A emerged as promising anti-CHOL candidates. So, this study offered a reference for the treatment of CHOL and the development of anti-CHOL drugs.PMID:38387122 | DOI:10.1016/j.compbiolchem.2024.108030 (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - February 22, 2024 Category: Bioinformatics Authors: Yuting Zhao Junfeng Guo Source Type: research

Interactions between DNA and the acridine intercalator: A computational study
Comput Biol Chem. 2024 Feb 12;109:108029. doi: 10.1016/j.compbiolchem.2024.108029. Online ahead of print.ABSTRACTCancer is a global public health problem characterized by deviations in the mechanisms that control cell proliferation, resulting in mutations and variations in the structure of DNA. The mechanisms of action of chemotherapeutic drugs are related to their interactions and binding with DNA; consequently, the development of antineoplastic agents that target DNA has extensively focused on use of acridine, a heterocyclic molecule that binds to deoxyribonucleic acid via intercalation, a process that modifies DNA and m...
Source: Computational Biology and Chemistry - February 22, 2024 Category: Bioinformatics Authors: Thaynara Guimar ães Miranda Nicolas Nascimento Ciribelli Murielly Fernanda Ribeiro Bihain Anna Karla Dos Santos Pereira Grasiele Soares Cavallini Douglas Henrique Pereira Source Type: research

Integrated study reveals mechanism of Tripterygium Wilfordii against cholangiocarcinoma based on bioinformatics approaches and molecular dynamics simulation
CONCLUSION: This study identified the therapeutic role and predicted the mechanism of TW against CHOL, where TW may combat CHOL through the regulation of metabolic conditions of the body, bile acid secretion, xenobiotics metabolism, and the inflammatory response. Celastrol, triptonide, triptolide and wilforlide A emerged as promising anti-CHOL candidates. So, this study offered a reference for the treatment of CHOL and the development of anti-CHOL drugs.PMID:38387122 | DOI:10.1016/j.compbiolchem.2024.108030 (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - February 22, 2024 Category: Bioinformatics Authors: Yuting Zhao Junfeng Guo Source Type: research