CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides
Brief Bioinform. 2024 Mar 27;25(3):bbae190. doi: 10.1093/bib/bbae190.ABSTRACTCyclic peptides offer a range of notable advantages, including potent antibacterial properties, high binding affinity and specificity to target molecules, and minimal toxicity, making them highly promising candidates for drug development. However, a comprehensive database that consolidates both synthetically derived and naturally occurring cyclic peptides is conspicuously absent. To address this void, we introduce CyclicPepedia (https://www.biosino.org/iMAC/cyclicpepedia/), a pioneering database that encompasses 8744 known cyclic peptides. This re...
Source: Briefings in Bioinformatics - April 28, 2024 Category: Bioinformatics Authors: Lei Liu Liu Yang Suqi Cao Zhigang Gao Bin Yang Guoqing Zhang Ruixin Zhu Dingfeng Wu Source Type: research
CPPLS-MLP: a method for constructing cell-cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data
Brief Bioinform. 2024 Mar 27;25(3):bbae198. doi: 10.1093/bib/bbae198.ABSTRACTIn the growth and development of multicellular organisms, the immune processes of the immune system and the maintenance of the organism's internal environment, cell communication plays a crucial role. It exerts a significant influence on regulating internal cellular states such as gene expression and cell functionality. Currently, the mainstream methods for studying intercellular communication are focused on exploring the ligand-receptor-transcription factor and ligand-receptor-subunit scales. However, there is relatively limited research on the a...
Source: Briefings in Bioinformatics - April 28, 2024 Category: Bioinformatics Authors: Tianjiao Zhang Zhenao Wu Liangyu Li Jixiang Ren Ziheng Zhang Guohua Wang Source Type: research
Classical molecular dynamics simulation identifies catechingallate as a promising antiviral polyphenol against MPOX palmitoylated surface protein
Comput Biol Chem. 2024 Apr 12;110:108070. doi: 10.1016/j.compbiolchem.2024.108070. Online ahead of print.ABSTRACTCumulative global prevalence of the emergent monkeypox (MPX) infection in the non-endemic countries has been professed as a global public health predicament. Lack of effective MPX-specific treatments sets the baseline for designing the current study. This research work uncovers the effective use of known antiviral polyphenols against MPX viral infection, and recognises their mode of interaction with the target F13 protein, that plays crucial role in formation of enveloped virions. Herein, we have employed state-...
Source: Computational Biology and Chemistry - April 28, 2024 Category: Bioinformatics Authors: Sarbani Mishra Madhusmita Rout Mahender Kumar Singh Budheswar Dehury Sanghamitra Pati Source Type: research
Identification of novel CA IX inhibitor: Pharmacophore modeling, docking, DFT, and dynamic simulation
Comput Biol Chem. 2024 Apr 17;110:108073. doi: 10.1016/j.compbiolchem.2024.108073. Online ahead of print.ABSTRACTHuman Carbonic anhydrase IX (hCA IX) is found to be an essential biomarker for the treatment of hypoxic tumors in both the early and metastatic stages of cancer. Due to its active function in maintaining pH levels and overexpression in hypoxic conditions, hCA IX inhibitors can be a potential candidate specifically designed to target cancer development at various stages. In search of selective hCA IX inhibitors, we developed a pharmacophore model from the existing natural product inhibitors with IC50 values less ...
Source: Computational Biology and Chemistry - April 28, 2024 Category: Bioinformatics Authors: Shakthi Devi Packiapalavesam Venkatesan Saravanan Anand A Mahajan Mikhlid H Almutairi Bader O Almutairi Jesu Arockiaraj Muthu Kumaradoss Kathiravan S Karthick Raja Namasivayam Source Type: research
A metagenome-wide association study of gut microbiome in patients with AMD, ASD, RA, T2D & amp; VKH diseases
Comput Biol Chem. 2024 Apr 20;110:108076. doi: 10.1016/j.compbiolchem.2024.108076. Online ahead of print.ABSTRACTClinical studies have already illustrated the associations between gut microbes and diseases, yet fundamental questions remain unclear that how we can universalize this knowledge. Considering the important role of human gut microbial composition in maintaining overall health, it is important to understand the microbial diversity and altered disease conditions of the human gut. Metagenomics provides a way to analyze and understand the microbes and their role in a community manner. It provides qualitative as well ...
Source: Computational Biology and Chemistry - April 28, 2024 Category: Bioinformatics Authors: Shivani Tyagi Pramod Katara Source Type: research
The role of the active site lysine residue on FAD reduction by NADPH in glutathione reductase
Comput Biol Chem. 2024 Apr 16;110:108075. doi: 10.1016/j.compbiolchem.2024.108075. Online ahead of print.ABSTRACTGlutathione reductase (GR) is a two dinucleotide binding domain flavoprotein (tDBDF) that catalyzes the reduction of glutathione disulfide to glutathione coupled to the oxidation of NADPH to NADP+. An interesting feature of GR and other tDBDFs is the presence of a lysine residue (Lys-66 in human GR) at the active site, which interacts with the flavin group, but has an unknown function. To better understand the role of this residue, the dynamics of GR was studied using molecular dynamics simulations, and the reac...
Source: Computational Biology and Chemistry - April 28, 2024 Category: Bioinformatics Authors: Jenner Bonanata Source Type: research
In-silico screening and identification of glycomimetic as potential human sodium-glucose co-transporter 2 inhibitor
Comput Biol Chem. 2024 Apr 13;110:108074. doi: 10.1016/j.compbiolchem.2024.108074. Online ahead of print.ABSTRACTSodium-glucose co-transporter 2 (SGLT2) is one of the important targets against type II diabetes mellitus. A typical SGLT2 inhibitor acts by inhibiting glucose reabsorption, thus lowering the blood glucose level. Unlike SGLT1, SGLT2 is responsible for almost 90% glucose reabsorption from glomerular filtrate. The current SGLT2 inhibitors include gliflozins, often prescribed as second or third-line agents in diabetes mellitus. The SGLT2 inhibitors also benefit patients with heart and kidney disease. Due to instabi...
Source: Computational Biology and Chemistry - April 28, 2024 Category: Bioinformatics Authors: Prerna Ganwir Rajendra Bhadane Ganesh U Chaturbhuj Source Type: research
Modelling the Impact of NETosis During the Initial Stage of Systemic Lupus Erythematosus
Bull Math Biol. 2024 Apr 28;86(6):66. doi: 10.1007/s11538-024-01291-3.ABSTRACTThe development of autoimmune diseases often takes years before clinical symptoms become detectable. We propose a mathematical model for the immune response during the initial stage of Systemic Lupus Erythematosus which models the process of aberrant apoptosis and activation of macrophages and neutrophils. NETosis is a type of cell death characterised by the release of neutrophil extracellular traps, or NETs, containing material from the neutrophil's nucleus, in response to a pathogenic stimulus. This process is hypothesised to contribute to the ...
Source: Bulletin of Mathematical Biology - April 28, 2024 Category: Bioinformatics Authors: Vladimira Suvandjieva Ivanka Tsacheva Marlene Santos Georgios Kararigas Peter Rashkov Source Type: research
Differentiating stable and unstable protein using convolution neural network and molecular dynamics simulations
In this study, a machine learning (ML) predictive model was developed to estimate these four parameters using the primary sequence of the protein. The shortfall of available tools for protein stability prediction based on multiple parameters propelled the completion of this study. Convolutional Neural Network (CNN) with multiple layers was adopted to develop a more reliable ML model. Individual predictive models were prepared for each property, and all the prepared models showed results with high accuracy. The R2 (coefficient of determination) of these models were 0.79, 0.78, 0.92 and 0.92, respectively, for ΔG, ΔCp, Tm ...
Source: Computational Biology and Chemistry - April 27, 2024 Category: Bioinformatics Authors: Shreyansh Suyash Akshat Jha Priyasha Maitra Parveen Punia Avinash Mishra Source Type: research
Heterogeneous graph inference with range constrainted L < sub > 2,1 < /sub > -collaborative matrix factorization for small molecule-miRNA association prediction
Comput Biol Chem. 2024 Apr 20;110:108078. doi: 10.1016/j.compbiolchem.2024.108078. Online ahead of print.ABSTRACTMicroRNAs (miRNAs) play a vital role in regulating gene expression and various biological processes. As a result, they have been identified as effective targets for small molecule (SM) drugs in disease treatment. Heterogeneous graph inference stands as a classical approach for predicting SM-miRNA associations, showcasing commendable convergence accuracy and speed. However, most existing methods do not adequately address the inherent sparsity in SM-miRNA association networks, and imprecise SM/miRNA similarity met...
Source: Computational Biology and Chemistry - April 27, 2024 Category: Bioinformatics Authors: Shudong Wang Tiyao Liu Chuanru Ren Yawu Zhao Sibo Qiao Yuanyuan Zhang Shanchen Pang Source Type: research
POLAT: Protein function prediction based on soft mask graph network and residue-Label ATtention
Comput Biol Chem. 2024 Apr 18;110:108064. doi: 10.1016/j.compbiolchem.2024.108064. Online ahead of print.ABSTRACTMOTIVATION: Elucidating protein function is a central problem in biochemistry, genetics, and molecular biology. Developing computational methods for protein function prediction is critical due to the significant gap between sequence and functional data. Recent advances in protein structure prediction, which strongly correlates with function, make it feasible to use structure to predict function. However, current structure-based methods overlook the fact that individual residues may contribute differently to the ...
Source: Computational Biology and Chemistry - April 27, 2024 Category: Bioinformatics Authors: Yang Liu Yi Zhang ZiHao Chen Jing Peng Source Type: research
Optimizing spatio-temporal correlation structures for modeling food security in Africa: a simulation-based investigation
This study investigates the impact of spatio- temporal correlation using four spatio-temporal models: Spatio-Temporal Poisson Linear Trend Model (SPLTM), Poisson Temporal Model (TMS), Spatio-Temporal Poisson A... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 27, 2024 Category: Bioinformatics Authors: Adusei Bofa and Temesgen Zewotir Tags: Research Source Type: research
Data-balanced transformer for accelerated ionizable lipid nanoparticles screening in mRNA delivery
Brief Bioinform. 2024 Mar 27;25(3):bbae186. doi: 10.1093/bib/bbae186.ABSTRACTDespite the widespread use of ionizable lipid nanoparticles (LNPs) in clinical applications for messenger RNA (mRNA) delivery, the mRNA drug delivery system faces an efficient challenge in the screening of LNPs. Traditional screening methods often require a substantial amount of experimental time and incur high research and development costs. To accelerate the early development stage of LNPs, we propose TransLNP, a transformer-based transfection prediction model designed to aid in the selection of LNPs for mRNA drug delivery systems. TransLNP uses...
Source: Briefings in Bioinformatics - April 26, 2024 Category: Bioinformatics Authors: Kun Wu Xiulong Yang Zixu Wang Na Li Jialu Zhang Lizhuang Liu Source Type: research
Prior knowledge-guided multilevel graph neural network for tumor risk prediction and interpretation via multi-omics data integration
Brief Bioinform. 2024 Mar 27;25(3):bbae184. doi: 10.1093/bib/bbae184.ABSTRACTThe interrelation and complementary nature of multi-omics data can provide valuable insights into the intricate molecular mechanisms underlying diseases. However, challenges such as limited sample size, high data dimensionality and differences in omics modalities pose significant obstacles to fully harnessing the potential of these data. The prior knowledge such as gene regulatory network and pathway information harbors useful gene-gene interaction and gene functional module information. To effectively integrate multi-omics data and make full use ...
Source: Briefings in Bioinformatics - April 26, 2024 Category: Bioinformatics Authors: Hongxi Yan Dawei Weng Dongguo Li Yu Gu Wenji Ma Qingjie Liu Source Type: research
DEGAP: Dynamic elongation of a genome assembly path
Brief Bioinform. 2024 Mar 27;25(3):bbae194. doi: 10.1093/bib/bbae194.ABSTRACTGenome assembly remains to be a major task in genomic research. Despite the development over the past decades of different assembly software programs and algorithms, it is still a great challenge to assemble a complete genome without any gaps. With the latest DNA circular consensus sequencing (CCS) technology, several assembly programs can now build a genome from raw sequencing data to contigs; however, some complex sequence regions remain as unresolved gaps. Here, we present a novel gap-filling software, DEGAP (Dynamic Elongation of a Genome Asse...
Source: Briefings in Bioinformatics - April 26, 2024 Category: Bioinformatics Authors: Yicheng Huang Ziyuan Wang Monica A Schmidt Handong Su Lizhong Xiong Jianwei Zhang Source Type: research
