keyword
https://read.qxmd.com/read/38536676/exploring-the-knowledge-of-an-outstanding-protein-to-protein-interaction-transformer
#1
JOURNAL ARTICLE
Sen Yang, Peng Cheng, Lingli Ju, Yang Liu, Dawei Feng, Shengqi Wang
Protein-to-protein interaction (PPI) prediction aims to predict whether two given proteins interact or not. Compared with traditional experimental methods of high cost and low efficiency, the current deep learning based approach makes it possible to discover massive potential PPIs from large-scale databases. However, deep PPI prediction models perform poorly on unseen species, as their proteins are not in the training set. Targetting on this issue, the paper first proposes PPITrans, a Transformer based PPI prediction model that exploits a language model pre-trained on proteins to conduct binary PPI prediction...
March 27, 2024: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://read.qxmd.com/read/38534847/application-of-machine-learning-in-the-quantitative-analysis-of-the-surface-characteristics-of-highly-abundant-cytoplasmic-proteins-toward-ai-based-biomimetics
#2
JOURNAL ARTICLE
Jooa Moon, Guanghao Hu, Tomohiro Hayashi
Proteins in the crowded environment of human cells have often been studied regarding nonspecific interactions, misfolding, and aggregation, which may cause cellular malfunction and disease. Specifically, proteins with high abundance are more susceptible to these issues due to the law of mass action. Therefore, the surfaces of highly abundant cytoplasmic (HAC) proteins directly exposed to the environment can exhibit specific physicochemical, structural, and geometrical characteristics that reduce nonspecific interactions and adapt to the environment...
March 6, 2024: Biomimetics
https://read.qxmd.com/read/38534687/navigating-the-chemical-space-of-enr-inhibitors-a-comprehensive-analysis
#3
JOURNAL ARTICLE
Vid Kuralt, Rok Frlan
Antimicrobial resistance is a global health threat that requires innovative strategies against drug-resistant bacteria. Our study focuses on enoyl-acyl carrier protein reductases (ENRs), in particular FabI, FabK, FabV, and InhA, as potential antimicrobial agents. Despite their promising potential, the lack of clinical approvals for inhibitors such as triclosan and isoniazid underscores the challenges in achieving preclinical success. In our study, we curated and analyzed a dataset of 1412 small molecules recognized as ENR inhibitors, investigating different structural variants...
March 11, 2024: Antibiotics
https://read.qxmd.com/read/38534443/new-genetic-variants-of-runx2-in-mexican-families-cause-cleidocranial-dysplasia
#4
JOURNAL ARTICLE
Jaime Toral López, Sandra Gómez Martinez, María Del Refugio Rivera Vega, Edgar Hernández-Zamora, Sergio Cuevas Covarrubias, Belem Arely Ibarra Castrejón, Luz María González Huerta
Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal dysplasia characterized by persistent open skull sutures with bulging calvaria, hypoplasia, or aplasia of clavicles permitting abnormal opposition of the shoulders; wide public symphysis; short middle phalanx of the fifth fingers; and vertebral, craniofacial, and dental anomalies. It is a rare disease, with a prevalence of 1-9/1,000,000, high penetrance, and variable expression. The gene responsible for CCD is the Runt-related transcription factor 2 ( RUNX2 ) gene...
March 8, 2024: Biology
https://read.qxmd.com/read/38534362/repurposing-drugs-for-senotherapeutic-effect-potential-senomorphic-effects-of-female-synthetic-hormones
#5
JOURNAL ARTICLE
Laura R Bramwell, Ryan Frankum, Lorna W Harries
Repurposing previously approved drugs may fast track the route to the clinic for potential senotherapeutics and improves the inefficiency of the clinical drug development pipeline. We performed a repurposing screen of 240 clinically approved molecules in human primary dermal fibroblasts for their effects on CDKN2A expression. Molecules demonstrating effects on CDKN2A expression underwent secondary screening for senescence-associated beta galactosidase (SAB) activity, based on effect size, direction, and/or molecule identity...
March 15, 2024: Cells
https://read.qxmd.com/read/38532339/hippo-histogram-based-pseudo-potential-for-scoring-protein-ssrna-fragment-based-docking-poses
#6
JOURNAL ARTICLE
Anna Kravchenko, Sjoerd Jacob de Vries, Malika Smaïl-Tabbone, Isaure Chauvot de Beauchene
BACKGROUND: The RNA-Recognition motif (RRM) is a protein domain that binds single-stranded RNA (ssRNA) and is present in as much as 2% of the human genome. Despite this important role in biology, RRM-ssRNA interactions are very challenging to study on the structural level because of the remarkable flexibility of ssRNA. In the absence of atomic-level experimental data, the only method able to predict the 3D structure of protein-ssRNA complexes with any degree of accuracy is ssRNA'TTRACT, an ssRNA fragment-based docking approach using ATTRACT...
March 26, 2024: BMC Bioinformatics
https://read.qxmd.com/read/38532317/cosap-comparative-sequencing-analysis-platform
#7
JOURNAL ARTICLE
Mehmet Arif Ergun, Omer Cinal, Berkant Bakışlı, Abdullah Asım Emül, Mehmet Baysan
BACKGROUND: Recent improvements in sequencing technologies enabled detailed profiling of genomic features. These technologies mostly rely on short reads which are merged and compared to reference genome for variant identification. These operations should be done with computers due to the size and complexity of the data. The need for analysis software resulted in many programs for mapping, variant calling and annotation steps. Currently, most programs are either expensive enterprise software with proprietary code which makes access and verification very difficult or open-access programs that are mostly based on command-line operations without user interfaces and extensive documentation...
March 26, 2024: BMC Bioinformatics
https://read.qxmd.com/read/38532297/pycom-a-python-library-for-large-scale-analysis-of-residue-residue-coevolution-data
#8
JOURNAL ARTICLE
Philipp Bibik, Sabriyeh Alibai, Alessandro Pandini, Sarath Chandra Dantu
MOTIVATION: Computational methods to detect correlated amino acid positions in proteins have become a valuable tool to predict intra and inter-residue protein contacts, protein structures, and effects of mutation on protein stability and function. While there are many tools and webservers to compute coevolution scoring matrices, there is no central repository of alignments and coevolution matrices for large-scale studies and pattern detection leveraging on structural and biological annotation already available in UniProt...
March 26, 2024: Bioinformatics
https://read.qxmd.com/read/38532295/pycomo-a-python-package-for-community-metabolic-model-creation-and-analysis
#9
JOURNAL ARTICLE
Michael Predl, Marianne Mießkes, Thomas Rattei, Jürgen Zanghellini
SUMMARY: PyCoMo is a python package for quick and easy generation of genome-scale compartmentalised community metabolic models that are compliant with current openCOBRA file formats. The resulting models can be used to predict (i) the maximum growth rate at a given abundance profile, (ii) the feasible community compositions at a given growth rate, and (iii) all exchange metabolites and cross-feeding interactions in a community metabolic model independent of the abundance profile; we demonstrate PyCoMo's capability by analysing methane production in a previously published simplified biogas community metabolic model (Koch et al...
March 26, 2024: Bioinformatics
https://read.qxmd.com/read/38530977/hypertmo-a-trusted-multi-omics-integration-framework-based-on-hypergraph-convolutional-network-for-patient-classification
#10
JOURNAL ARTICLE
Haohua Wang, Kai Lin, Qiang Zhang, Jinlong Shi, Xinyu Song, Jue Wu, Chenghui Zhao, Kunlun He
MOTIVATION: The rapid development of high-throughput biomedical technologies can provide researchers with detailed multi-omics data. The multi-omics integrated analysis approach based on machine learning contributes a more comprehensive perspective to human disease research. However, there are still significant challenges in representing single-omics data and integrating multi-omics information. RESULTS: This paper presents HyperTMO, a Trusted Multi-Omics integration framework based on Hypergraph convolutional network for patient classification...
March 26, 2024: Bioinformatics
https://read.qxmd.com/read/38530779/molemcl-a-multi-level-contrastive-learning-framework-for-molecular-pre-training
#11
JOURNAL ARTICLE
Xinyi Zhang, Yanni Xu, Changzhi Jiang, Lian Shen, Xiangrong Liu
MOTIVATION: Molecular representation learning plays an indispensable role in crucial tasks such as property prediction and drug design. Despite the notable achievements of Molecular Pre-training Models (MPMs), current methods often fail to capture both the structural and feature semantics of molecular graphs. Moreover, while graph contrastive learning has unveiled new prospects, existing augmentation techniques often struggle to retain their core semantics. To overcome these limitations, we propose a gradient-compensated encoder parameter perturbation approach, ensuring efficient and stable feature augmentation...
March 26, 2024: Bioinformatics
https://read.qxmd.com/read/38530079/molecular-and-structural-insights-into-buffalo-interleukin-17a
#12
JOURNAL ARTICLE
Savita Budania, Surinder Kumar Kadian, Karuppiah Kanagarajadurai, Vikas Yadav, Aman Kumar, Akhil Kumar Gupta
Interleukin-17A is a pro-inflammatory cytokine that plays a key role in the immune response to many pathogens and implicated in autoimmune diseases. This molecule is also involved in providing protection to many bacterial and fungal infections of gastro-intestinal tract and respiratory mucosa. Although molecular aspect of IL-17A has been studied in few species, no data are available for buffalo, which is one of the major sources of milk production in India. Therefore, in the present study, IL-17A gene of Indian Murrah Buffalo origin was cloned, expressed, and analyzed using bioinformatic tools...
March 26, 2024: Journal of Interferon & Cytokine Research
https://read.qxmd.com/read/38529847/tepotinib-and-tivantinib-as-potential-inhibitors-for-the-serine-threonine-kinase-of-the-mpox-virus-insights-from-structural-bioinformatics-analysis
#13
JOURNAL ARTICLE
Jameel M Abduljalil, Abdo A Elfiky, Maha M AlKhazindar
The serine/threonine kinase (STK) plays a central role as the primary kinase in poxviruses, directing phosphoryl transfer reactions. Such reactions are pivotal for the activation of certain proteins during viral replication, assembly, and maturation. Therefore, targeting this key protein is anticipated to impede virus replication. In this work, a structural bioinformatics approach was employed to evaluate the potential of drug-like kinase inhibitors in binding to the ATP-binding pocket on the STK of the Mpox virus...
March 26, 2024: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/38529759/what-is-new-in-fungidb-a-web-based-bioinformatics-platform-for-omics-scale-data-analysis-for-fungal-and-oomycete-species
#14
JOURNAL ARTICLE
Evelina Y Basenko, Achchuthan Shanmugasundram, Ulrike Böhme, David Starns, Paul A Wilkinson, Helen R Davison, Kathryn Crouch, Gareth Maslen, Omar S Harb, Beatrice Amos, Mary Ann McDowell, Jessica C Kissinger, David S Roos, Andrew Jones
FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e...
March 26, 2024: Genetics
https://read.qxmd.com/read/38528516/peli1-key-players-in-the-oncogenic-characteristics-of-pancreatic-cancer
#15
JOURNAL ARTICLE
Xiaobin Fei, Changhao Zhu, Peng Liu, Songbai Liu, Likun Ren, Rishang Lu, Junyi Hou, Yongjia Gao, Xing Wang, Yaozhen Pan
BACKGROUND: Pancreatic cancer (PC) is a highly malignant gastrointestinal tumor, which is characterized by difficulties in early diagnosis, early metastasis, limited therapeutic response and a grim prognosis. Therefore, it is imperative to explore potential therapeutic targets for PC. Currently, although the involvement of the Pellino E3 Ubiquitin Protein Ligase 1 (PELI1) in the human growth of some malignant tumors has been demonstrated, its association with PC remains uncertain. METHODS: Bioinformatics, qRT-PCR, Western blot and IHC were used to detect the expression of PELI1 in pancreas or PC tissues and cells at mRNA and protein levels...
March 25, 2024: Journal of Experimental & Clinical Cancer Research: CR
https://read.qxmd.com/read/38527035/hmgr-and-chs-gene-cloning-characterizations-and-tissue-specific-expressions-in-polygala-tenuifolia-willd
#16
JOURNAL ARTICLE
Yang Liu, Xiaofang Ma, Fuying Mao, Jinmiao Qiu, Jingyi Bi, Xiaowei Li, Xian Gu, Yuguang Zheng, Yunsheng Zhao
Triterpenoid saponins and flavonoids have several pharmacological activities against P. tenuifolia. The 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) and chalcone synthase (CHS) are the rate-limiting enzymes of triterpenoid saponin and flavonoid biosynthesis, respectively. In this study, HMGR and CHS genes were cloned from P. tenuifolia, and their bioinformatics analyses and tissue-specific expression were investigated. The results showed that the HMGR and CHS genes were successfully cloned, separately named the PtHMGR gene (NCBI accession: MK424118) and PtCHS gene (NCBI accession: MK424117)...
2024: PloS One
https://read.qxmd.com/read/38526734/multidisciplinary-methods-for-screening-toxic-proteins-from-phages-and-their-potential-molecular-targets
#17
JOURNAL ARTICLE
Xing Wan, Mikael Skurnik
This chapter presents a comprehensive methodology for the identification, characterization, and functional analyses of potentially toxic hypothetical proteins of unknown function (toxHPUFs) in phages. The methods begin with in vivo toxicity verification of toxHPUFs in bacterial hosts, utilizing conventional drop tests and following growth curves. Computational methods for structural and functional predictions of toxHPUFs are outlined, incorporating the use of tools such as Phyre2, HHpred, and AlphaFold2. To ascertain potential targets, a comparative genomic approach is described using bioinformatics toolkits for sequence alignment and functional annotation...
2024: Methods in Molecular Biology
https://read.qxmd.com/read/38525916/dynein-light-intermediate-chains-exhibit-different-arginine-methylation-patterns
#18
JOURNAL ARTICLE
Weiwen Bu, Jie Di, Junkui Zhao, Ruming Liu, Yue Wu, Jie Ran, Te Li
BACKGROUND: The motor protein dynein is integral to retrograde transport along microtubules and interacts with numerous cargoes through the recruitment of cargo-specific adaptor proteins. This interaction is mediated by dynein light intermediate chain subunits LIC1 (DYNC1LI1) and LIC2 (DYNC1LI2), which govern the adaptor binding and are present in distinct dynein complexes with overlapping and unique functions. METHODS: Using bioinformatics, we analyzed the C-terminal domains (CTDs) of LIC1 and LIC2, revealing similar structural features but diverse post-translational modifications (PTMs)...
March 25, 2024: Journal of Clinical Laboratory Analysis
https://read.qxmd.com/read/38525437/circulating-exosome-long-non-coding-rnas-are-associated-with-atrial-structural-remodeling-by-increasing-systemic-inflammation-in-atrial-fibrillation-patients
#19
JOURNAL ARTICLE
Yue Yuan, Xuejie Han, Xinbo Zhao, Haiyu Zhang, Asiia Vinograd, Xin Bi, Xiaoxu Duan, Yukai Cao, Qiang Gao, Jia Song, Li Sheng, Yue Li
BACKGROUND: Atrial fibrillation (AF) is the most common cardiac arrhythmia with severe clinical sequelae, but its genetic characteristic implicated in pathogenesis has not been completely clarified. Accumulating evidence has indicated that circulating exosomes and their carried cargoes, such as long non-coding RNAs (lncRNAs), involve in the progress of multiple cardiovascular diseases. However, their potential role as clinical biomarkers in AF diagnosis and prognosis remains unknown. METHODS: Herein, we conducted the sequence and bioinformatic analysis of circulating exosomes harvested from AF and sinus rhythm patients...
February 2024: Journal of Translational Internal Medicine
https://read.qxmd.com/read/38525326/role-of-integrin-%C3%AE-1-and-tenascin-c-mediate-tgf-smad2-3-signaling-in-chondrogenic-differentiation-of-bmscs-induced-by-type-i-collagen-hydrogel
#20
JOURNAL ARTICLE
Yuanjun Huang, Miao Sun, Zhenhui Lu, Qiuling Zhong, Manli Tan, Qingjun Wei, Li Zheng
Cartilage defects may lead to severe degenerative joint diseases. Tissue engineering based on type I collagen hydrogel that has chondrogenic potential is ideal for cartilage repair. However, the underlying mechanisms of chondrogenic differentiation driven by type I collagen hydrogel have not been fully clarified. Herein, we explored potential collagen receptors and chondrogenic signaling pathways through bioinformatical analysis to investigate the mechanism of collagen-induced chondrogenesis. Results showed that the super enhancer-related genes induced by collagen hydrogel were significantly enriched in the TGF-β signaling pathway, and integrin-β1 (ITGB1), a receptor of collagen, was highly expressed in bone marrow mesenchymal stem cells (BMSCs)...
2024: Regenerative Biomaterials
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