A Regulatory Axis between Epithelial Splicing Regulatory Proteins and Estrogen Receptor α Modulates the Alternative Transcriptome of Luminal Breast Cancer.
PMID:35887187
TritiKBdb: A Functional Annotation Resource for Deciphering the Complete Interaction Networks in Wheat-Karnal Bunt Pathosystem.
PMID:35806459
Deciphering the Crosstalk Mechanisms of Wheat-Stem Rust Pathosystem: Genome-Scale Prediction Unravels Novel Host Targets.
PMID:35800602
Are transient protein-protein interactions more dispensable?
PMID:35404956
Predicting protein-protein interactions between banana and Fusarium oxysporum f. sp. cubense race 4 integrating sequence and domain homologous alignment and neural network verification.
PMID:35351140
Deciphering the Host-Pathogen Interactome of the Wheat-Common Bunt System: A Step towards Enhanced Resilience in Next Generation Wheat.
PMID:35269732
Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop.
PMID:35251063
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases.
PMID:34857024
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation.
PMID:34769335
Performance Assessment of the Network Reconstruction Approaches on Various Interactomes.
PMID:34676243
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
PMID:34370723
Predicting Protein-Protein Interactions Between Rice and Blast Fungus Using Structure-Based Approaches.
PMID:34367213
Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans.
PMID:34315882
Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis.
PMID:34162325
mPPI: a database extension to visualize structural interactome in a one-to-many manner.
PMID:34156447
Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins.
PMID:34133714
Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants.
PMID:34076240
Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs.
PMID:34012977
dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains.
PMID:33999210
Alternatively Splicing Interactomes Identify Novel Isoform-Specific Partners for NSD2.
PMID:33718354
The analysis on the human protein domain targets and host-like interacting motifs for the MERS-CoV and SARS-CoV/CoV-2 infers the molecular mimicry of coronavirus.
PMID:33596252
Family-specific analysis of variant pathogenicity prediction tools.
PMID:33575576
Large-scale survey and database of high affinity ligands for peptide recognition modules.
PMID:33438817
An Integrative Computational Approach for the Prediction of Human-Plasmodium Protein-Protein Interactions.
PMID:33426052
FilterDCA: Interpretable supervised contact prediction using inter-domain coevolution.
PMID:33035205
DIGGER: exploring the functional role of alternative splicing in protein interactions.
PMID:32976589
Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network.
PMID:32879328
Using collections of structural models to predict changes of binding affinity caused by mutations in protein-protein interactions.
PMID:32797645
Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein-Protein Association.
PMID:32679892
Protein-Protein Interactions Efficiently Modeled by Residue Cluster Classes.
PMID:32640745
Dynamic rewiring of the human interactome by interferon signaling.
PMID:32539747
A Systematic Test of Receptor Binding Kinetics for Ligands in Tumor Necrosis Factor Superfamily by Computational Simulations.
PMID:32150842
Pathway and network analysis of more than 2500 whole cancer genomes.
PMID:32024854
ProtCID: a data resource for structural information on protein interactions.
PMID:32024829
Domain-mediated interactions for protein subfamily identification.
PMID:31937869
Transcriptomic Insights into Innate Immunity Responding to Red Rot Disease in Red Alga Pyropia yezoensis.
PMID:31783543
Enriching Human Interactome with Functional Mutations to Detect High-Impact Network Modules Underlying Complex Diseases.
PMID:31731769
Uncovering and characterizing splice variants associated with survival in lung cancer patients.
PMID:31652257
Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.
PMID:31515488
Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries.
PMID:31364989
ProtDCal-Suite: A web server for the numerical codification and functional analysis of proteins.
PMID:31271472
Evolution of protein kinase substrate recognition at the active site.
PMID:31233486
Differential analysis of combinatorial protein complexes with CompleXChange.
PMID:31159772
Conserved phosphorylation hotspots in eukaryotic protein domain families.
PMID:31036831
Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism.
PMID:30815000
Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes.
PMID:30759076
Building Bridges Between Structural and Network-Based Systems Biology.
PMID:30656572
Computational studies of protein-protein dissociation by statistical potential and coarse-grained simulations: a case study on interactions between colicin E9 endonuclease and immunity proteins.
PMID:30652698
Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing.
PMID:30547433
Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.
PMID:30535108
SLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions.
PMID:30402352
Genomic data integration systematically biases interactome mapping.
PMID:30332399
Proteome-wide analysis of human motif-domain interactions mapped on influenza a virus.
PMID:29940841
A Novel Geometry-Based Approach to Infer Protein Interface Similarity.
PMID:29844500
Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation.
PMID:29390084
Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.
PMID:29322920
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes.
PMID:29186384
The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery.
PMID:29186335
A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE).
PMID:29061110
Algorithms for matching partially labelled sequence graphs.
PMID:29021818
Scipion web tools: Easy to use cryo-EM image processing over the web.
PMID:28971542
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology.
PMID:28874689
Protein-Protein Interactions in Virus-Host Systems.
PMID:28861068
Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing.
PMID:28846689
In silico structure-based approaches to discover protein-protein interaction-targeting drugs.
PMID:28802714
Genetic and functional characterization of disease associations explains comorbidity.
PMID:28740175
Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare.
PMID:28376810
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis.
PMID:28376709
Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions.
PMID:28253857
The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies.
PMID:28205554
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone.
PMID:27965389
Prediction of Protein-Protein Interactions by Evidence Combining Methods.
PMID:27879651
Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks.
PMID:27403431
AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana.
PMID:27338257
K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer.
PMID:27148219
Maximum margin classifier working in a set of strings.
PMID:27118908
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.
PMID:26871637
Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02.
PMID:26782814
3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.
PMID:26772592
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.
PMID:26708988
Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling.
PMID:26549015
FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events.
PMID:26384373
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes.
PMID:26307061
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors.
PMID:26111183
QSLiMFinder: improved short linear motif prediction using specific query protein data.
PMID:25792551
Decomposing the space of protein quaternary structures with the interface fragment pair library.
PMID:25592649
Protein structure annotation resources.
PMID:25502191
Computational prediction of protein interactions related to the invasion of erythrocytes by malarial parasites.
PMID:25433733
Exploiting holistic approaches to model specificity in protein phosphorylation.
PMID:25324856
Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks.
PMID:25299147
Elucidating the genotype-phenotype relationships and network perturbations of human shared and specific disease genes from an evolutionary perspective.
PMID:25287147
In silico modeling of human α2C-adrenoreceptor interaction with filamin-2.
PMID:25110951
The Protein Data Bank archive as an open data resource.
PMID:25062767
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.
PMID:24316579