Search Results - "interaction"

Mapping the BCSC-1 interactome in breast cancer.

Authors: Ma Y Zhang Q Ju J et al.

Source: Scientific reports [Sci Rep] 2025 Oct 21; Vol. 15 (1), pp. 36728. Date of Electronic Publication: 2025 Oct 21.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH Terms: Breast Neoplasms*/metabolism , Breast Neoplasms*/pathology , Breast Neoplasms*/genetics , Protein Interaction Maps* , Neoplasm Proteins*/metabolism , Neoplasm Proteins*/genetics, Humans ; Female ; MCF-7 Cells ; Cell Movement ; Protein Interaction Mapping ; Protein Binding ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic

The relationship between interfacial overlap and functional divergence in the yeast protein-protein interaction network.

Authors: Han Y Ghadie M Xia Y

Source: Structure (London, England : 1993) [Structure] 2025 Dec 04; Vol. 33 (12), pp. 2164-2176.e2. Date of Electronic Publication: 2025 Sep 17.

Publication Type: Journal Article

Journal Info: Publisher: Cell Press Country of Publication: United States NLM ID: 101087697 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-4186 (Electronic) Linking ISSN: 09692126 NLM ISO Abbreviation: Structure Subsets: MEDLINE

MeSH Terms: Protein Interaction Maps* , Saccharomyces cerevisiae*/metabolism , Saccharomyces cerevisiae*/genetics , Saccharomyces cerevisiae Proteins*/metabolism , Saccharomyces cerevisiae Proteins*/chemistry , Saccharomyces cerevisiae Proteins*/genetics, Protein Binding ; Protein Interaction Mapping ; Models, Molecular

Towards a phylogenetically informed approach to solving protein-protein interactions.

Authors: Lim CS Mace P Fineran PC et al.

Source: Biochemical Society transactions [Biochem Soc Trans] 2025 Dec 03; Vol. 53 (6). Date of Electronic Publication: 2025 Dec 03.

Publication Type: Journal Article; Review

Journal Info: Publisher: Portland Press On The Behalf Of The Biochemical Society Country of Publication: England NLM ID: 7506897 Publication Model: Electronic Cited Medium: Internet ISSN: 1470-8752 (Electronic) Linking ISSN: 03005127 NLM ISO Abbreviation: Biochem Soc Trans Subsets: MEDLINE

MeSH Terms: Phylogeny* , Protein Interaction Mapping*/methods , Proteins*/metabolism , Proteins*/chemistry, Humans ; Databases, Protein ; Computational Biology/methods ; Animals ; Machine Learning ; Protein Binding ; Protein Interaction Maps

MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages.

Authors: Pazicky S Tjia S Farias GB et al.

Source: Nature microbiology [Nat Microbiol] 2025 Dec; Vol. 10 (12), pp. 3229-3244. Date of Electronic Publication: 2025 Nov 28.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101674869 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2058-5276 (Electronic) Linking ISSN: 20585276 NLM ISO Abbreviation: Nat Microbiol Subsets: MEDLINE

MeSH Terms: Plasmodium falciparum*/growth & development , Plasmodium falciparum*/metabolism , Plasmodium falciparum*/genetics , Protozoan Proteins*/metabolism , Protozoan Proteins*/genetics , Erythrocytes*/parasitology , Protein Interaction Mapping*/methods, Proteome ; Humans ; Malaria, Falciparum/parasitology ; Protein Interaction Maps ; Proteomics/methods ; Life Cycle Stages

Comparative Analysis of Host-Pathogen Protein-Protein Interactions between Human and Various Strains of Mycobacterium Tuberculosis.

Authors: Verma D Mudgal B Tufchi N et al.

Source: Clinical laboratory [Clin Lab] 2025 Nov 01; Vol. 71 (11).

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: Clinical Laboratory Publications Country of Publication: Germany NLM ID: 9705611 Publication Model: Print Cited Medium: Internet ISSN: 1433-6510 (Print) Linking ISSN: 14336510 NLM ISO Abbreviation: Clin Lab Subsets: MEDLINE

MeSH Terms: Mycobacterium tuberculosis*/pathogenicity , Mycobacterium tuberculosis*/metabolism , Host-Pathogen Interactions* , Bacterial Proteins*/metabolism , Tuberculosis*/microbiology , Tuberculosis*/metabolism , Protein Interaction Maps*, Humans ; Protein Interaction Mapping/methods

Conserved interfaces mediate multiple protein-protein interactions in a prokaryotic metabolon.

Authors: Bhattacharyya S Ranganathan S Chowdhury S et al.

Source: Molecular systems biology [Mol Syst Biol] 2025 Nov; Vol. 21 (11), pp. 1490-1521. Date of Electronic Publication: 2025 Sep 03.

Publication Type: Journal Article

Journal Info: Publisher: EMBO Press Country of Publication: Germany NLM ID: 101235389 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1744-4292 (Electronic) Linking ISSN: 17444292 NLM ISO Abbreviation: Mol Syst Biol Subsets: MEDLINE

MeSH Terms: Escherichia coli*/metabolism , Escherichia coli*/genetics , Escherichia coli Proteins*/metabolism , Escherichia coli Proteins*/chemistry , Escherichia coli Proteins*/genetics , Protein Interaction Maps*, Metabolic Networks and Pathways ; Protein Binding ; Folic Acid/biosynthesis ; Protein Interaction Mapping/methods ; Molecular Dynamics Simulation ; Purines

Mapping Context-Aware Phosphosite Regulation of Protein-Protein Interactions Using Deep Learning and Pan-Cancer Proteomics.

Authors: Cai M Xiao Y Zheng J et al.

Source: Journal of chemical information and modeling [J Chem Inf Model] 2025 Oct 27; Vol. 65 (20), pp. 11255-11271. Date of Electronic Publication: 2025 Oct 10.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE

MeSH Terms: Deep Learning* , Proteomics* , Neoplasms*/metabolism , Neoplasms*/pathology , Protein Interaction Mapping*, Humans ; Phosphorylation ; Histone Deacetylase 1/metabolism ; Histone Demethylases/metabolism ; Cell Line, Tumor ; Protein Interaction Maps

Predicting protein-protein interactions in the human proteome.

Authors: Zhang J Humphreys IR Pei J et al.

Source: Science (New York, N.Y.) [Science] 2025 Oct 23; Vol. 390 (6771), pp. eadt1630. Date of Electronic Publication: 2025 Oct 23.

Publication Type: Journal Article

Journal Info: Publisher: American Association for the Advancement of Science Country of Publication: United States NLM ID: 0404511 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9203 (Electronic) Linking ISSN: 00368075 NLM ISO Abbreviation: Science Subsets: MEDLINE

MeSH Terms: Proteome*/chemistry , Proteome*/metabolism , Deep Learning* , Protein Interaction Mapping*/methods, Humans ; Sequence Alignment ; Protein Conformation ; Models, Molecular ; Protein Interaction Maps

Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation.

Authors: Wang P; Department of Computer Science, School of Artificial Intelligence, Chongqing Technology and Business University, No.19, Xuefu Ave, Nanan District, Chongqing, 400067, People's Republic of China. pengw@ctbu.edu.cn.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Oct 21; Vol. 26 (1), pp. 255. Date of Electronic Publication: 2025 Oct 21.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Algorithms* , Proteins*/metabolism , Proteins*/chemistry , Computational Biology*/methods , Protein Interaction Mapping*/methods, Databases, Protein ; Protein Interaction Maps

PPI-ID: Streamlining protein-protein interaction prediction through domain and SLiM mapping.

Authors: Goodwin HV Atkinson NS

Source: PLoS computational biology [PLoS Comput Biol] 2025 Oct 16; Vol. 21 (10), pp. e1013062. Date of Electronic Publication: 2025 Oct 16 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MeSH Terms: Protein Interaction Mapping*/methods , Proteins*/chemistry , Proteins*/metabolism , Computational Biology*/methods, Databases, Protein ; Models, Molecular ; Protein Interaction Domains and Motifs ; Software ; Algorithms ; Protein Binding ; Protein Conformation

Prediction and Evaluation of Coronavirus and Human Protein-Protein Interactions Integrating Five Different Computational Methods.

Authors: Li B Li X Tang X et al.

Source: Proteins [Proteins] 2025 Sep; Vol. 93 (9), pp. 1553-1570. Date of Electronic Publication: 2025 Apr 15.

Publication Type: Journal Article

Journal Info: Publisher: Wiley-Liss Country of Publication: United States NLM ID: 8700181 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1097-0134 (Electronic) Linking ISSN: 08873585 NLM ISO Abbreviation: Proteins Subsets: MEDLINE

MeSH Terms: Computational Biology*/methods , Protein Interaction Mapping*/methods , SARS-CoV-2*/metabolism , Viral Proteins*/metabolism , Viral Proteins*/chemistry, Humans ; Machine Learning ; Protein Interaction Maps ; COVID-19/virology ; COVID-19/metabolism ; Protein Interaction Domains and Motifs ; Databases, Protein

Establishing TurboID Proximity Labeling and mAID Conditional Knockdown System in Cryptosporidium parvum.

Authors: Xu R Sibley LD

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2026; Vol. 2978, pp. 299-316.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Cryptosporidium parvum*/genetics , Cryptosporidium parvum*/metabolism , Protozoan Proteins*/metabolism , Protozoan Proteins*/genetics , Gene Knockdown Techniques*/methods , Protein Interaction Mapping*/methods , Staining and Labeling*/methods, Protein Interaction Maps ; Indoleacetic Acids/pharmacology

diaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling.

Authors: Woods K Chan AM Rants'o TA et al.

Source: Journal of proteome research [J Proteome Res] 2025 Sep 05; Vol. 24 (9), pp. 4463-4477. Date of Electronic Publication: 2025 Aug 27.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE

MeSH Terms: Proteomics*/methods , Protein Kinases*/metabolism , Protein Interaction Mapping*/methods, Humans ; Cell Line, Tumor ; Mass Spectrometry/methods ; Signal Transduction ; Protein Interaction Maps ; Phosphorylation ; Algorithms ; Protein Kinase Inhibitors/pharmacology

Long-read sequencing to detect full-length protein-protein interactions.

Authors: Schaefer-Ramadan S Guan Y Ahmed AA et al.

Source: Scientific reports [Sci Rep] 2025 Jul 17; Vol. 15 (1), pp. 25967. Date of Electronic Publication: 2025 Jul 17.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH Terms: High-Throughput Nucleotide Sequencing*/methods , Protein Interaction Mapping*/methods , Proteins*/metabolism , Proteins*/genetics, Humans ; Two-Hybrid System Techniques ; Protein Binding ; Protein Interaction Maps

Advancing edge-based clustering and graph embedding for biological network analysis: a case study in RASopathies.

Authors: García-Criado F Seoane P Rojano E et al.

Source: Briefings in bioinformatics [Brief Bioinform] 2025 Jul 02; Vol. 26 (4).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

MeSH Terms: Protein Interaction Maps* , Computational Biology*/methods , ras Proteins*/genetics , ras Proteins*/metabolism , Noonan Syndrome*/genetics , Noonan Syndrome*/metabolism, Humans ; Algorithms ; Cluster Analysis ; Protein Interaction Mapping/methods ; Software

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge.

Authors: Park G Yoon BJ Luo X et al.

Source: Journal of computational biology : a journal of computational molecular cell biology [J Comput Biol] 2025 Jul; Vol. 32 (7), pp. 675-695. Date of Electronic Publication: 2025 May 19.

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: Mary Ann Liebert, Inc Country of Publication: United States NLM ID: 9433358 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1557-8666 (Electronic) Linking ISSN: 10665277 NLM ISO Abbreviation: J Comput Biol Subsets: MEDLINE

MeSH Terms: Computational Biology*/methods , Protein Interaction Mapping*/methods, Humans ; Gene Regulatory Networks ; Protein Interaction Maps ; Algorithms ; Large Language Models

PF-AGCN: an adaptive graph convolutional network for protein-protein interaction-based function prediction.

Authors: Yang S Su Y Lin Y et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Sep 01; Vol. 41 (9).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Protein Interaction Mapping*/methods , Neural Networks, Computer* , Software* , Proteins*/metabolism , Proteins*/chemistry , Computational Biology*/methods, Databases, Protein ; Gene Ontology ; Algorithms ; Protein Interaction Maps

GNNenrich: a novel method for pathway enrichment analysis based on graph neural network.

Authors: Mziou-Sallami M Roger P Gloaguen A et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Sep 01; Vol. 41 (9).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Neural Networks, Computer* , Protein Interaction Mapping*/methods , Computational Biology*/methods , Software*, Algorithms ; Protein Interaction Maps ; Databases, Protein ; Graph Neural Networks

Graph neural network integrated with pretrained protein language model for predicting human-virus protein-protein interactions.

Authors: Jiang L Yang X Guo X et al.

Source: Briefings in bioinformatics [Brief Bioinform] 2025 Aug 31; Vol. 26 (5).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

MeSH Terms: Neural Networks, Computer* , Viral Proteins*/metabolism , Viral Proteins*/chemistry , Computational Biology*/methods , Protein Interaction Mapping*/methods, Humans ; Host-Pathogen Interactions ; Protein Interaction Maps ; Graph Neural Networks

Large-scale protein interactome reveals lineage-specific genes driving plant-parasitic nematode adaptive innovations.

Authors: Huang G Wang K Li F et al.

Source: Science advances [Sci Adv] 2025 Aug 15; Vol. 11 (33), pp. eadt5107. Date of Electronic Publication: 2025 Aug 15.

Publication Type: Journal Article

Journal Info: Publisher: American Association for the Advancement of Science Country of Publication: United States NLM ID: 101653440 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2375-2548 (Electronic) Linking ISSN: 23752548 NLM ISO Abbreviation: Sci Adv Subsets: MEDLINE

MeSH Terms: Helminth Proteins*/metabolism , Helminth Proteins*/genetics , Protein Interaction Maps* , Nematoda*/genetics , Plants*/parasitology, Animals ; Host-Parasite Interactions/genetics ; Protein Interaction Mapping ; Plant Diseases/parasitology ; Two-Hybrid System Techniques