EciD

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EciD

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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EcID

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:42.839615

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ecid

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:42.839615

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Other names: EcID, ecid

Protein interaction predictions by several different methods

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Publications

More detailed information about this field from each metasource. ×

Computational methods for the prediction of protein interactions
PMID: 12127457

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:42.839615

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• Computational methods for the prediction of protein interactions PubMed citations: 98.

  98 articles citing: Computational methods for the prediction of protein interactions

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  Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes. PMID:34285778

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  SeRenDIP-CE: Sequence-based Interface Prediction for Conformational Epitopes. PMID:33974039

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  A critical perspective on Markov state model treatments of protein-protein association using coarse-grained simulations. PMID:33639768

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  2D Zernike polynomial expansion: Finding the protein-protein binding regions. PMID:33363707

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  A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins. PMID:33237964

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  WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data. PMID:32221380

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  A multi-scale coevolutionary approach to predict interactions between protein domains. PMID:31634362

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  Network reconstruction from infection cascades. PMID:30958195

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  Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082

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  Prediction of cassava protein interactome based on interolog method. PMID:29222529

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  ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer. PMID:28549153

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  Predicting protein-protein interactions via multivariate mutual information of protein sequences. PMID:27677692

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  Identification of Protein-Protein Interactions via a Novel Matrix-Based Sequence Representation Model with Amino Acid Contact Information. PMID:27669239

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  Great interactions: How binding incorrect partners can teach us about protein recognition and function. PMID:27287388

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  CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys. PMID:27166787

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  Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon. PMID:26882169

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  Identification of 14-3-3 Proteins Phosphopeptide-Binding Specificity Using an Affinity-Based Computational Approach. PMID:26828594

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  Sequence specificity between interacting and non-interacting homologs identifies interface residues--a homodimer and monomer use case. PMID:26449222

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  Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP. PMID:26278180

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  Quantifying the displacement of mismatches in multiple sequence alignment benchmarks. PMID:25993129

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  STRING v10: protein-protein interaction networks, integrated over the tree of life. PMID:25352553

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  Structure-based inhibition of protein-protein interactions. PMID:25253637

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  Prediction and functional analysis of the sweet orange protein-protein interaction network. PMID:25091279

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  Perturbation of the monomer-monomer interfaces of the benzoylformate decarboxylase tetramer. PMID:24956165

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  Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. PMID:24842992

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  Protein-protein interface detection using the energy centrality relationship (ECR) characteristic of proteins. PMID:24830938

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  Proteomics, metabolomics, and protein interactomics in the characterization of the molecular features of major depressive disorder. PMID:24733971

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  Chapter 4: Protein interactions and disease. PMID:23300410

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  PrePPI: a structure-informed database of protein-protein interactions. PMID:23193263

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  BCL::Fold--de novo prediction of complex and large protein topologies by assembly of secondary structure elements. PMID:23173050

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  Uncovering the co-evolutionary network among prokaryotic genes. PMID:22962457

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  A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. PMID:22937800

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  Analysis of domain-swapped oligomers reveals local sequence preferences and structural imprints at the linker regions and swapped interfaces. PMID:22848353

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  Simulated evolution of protein-protein interaction networks with realistic topology. PMID:22768057

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  Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399

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  Tools used to study how protein complexes are assembled in signaling cascades. PMID:22002082

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  Direct correlation analysis improves fold recognition. PMID:22000804

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  Bayesian inference for genomic data integration reduces misclassification rate in predicting protein-protein interactions. PMID:21829334

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  Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. PMID:21801404

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  Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. PMID:21767381

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  Networked-based characterization of extracellular matrix proteins from adult mouse pulmonary and aortic valves. PMID:21133377

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  iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. PMID:21130772

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  Yeast biological networks unfold the interplay of antioxidants, genome and phenotype, and reveal a novel regulator of the oxidative stress response. PMID:21049050

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  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058

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  Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins. PMID:20854660

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  Algorithmic and analytical methods in network biology. PMID:20836029

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  Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data. PMID:20817744

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  Development of a novel bioinformatics tool for in silico validation of protein interactions. PMID:20625507

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  Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach. PMID:20526429

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  Inference of functional relations in predicted protein networks with a machine learning approach. PMID:20376314

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  Construction and analysis of protein-protein interaction networks. PMID:20334628

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  Predicting the protein-protein interactions using primary structures with predicted protein surface. PMID:20122202

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  Structural and functional roles of coevolved sites in proteins. PMID:20066038

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  Phylogeny-guided interaction mapping in seven eukaryotes. PMID:19948065

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  BCL::contact-low confidence fold recognition hits boost protein contact prediction and de novo structure determination. PMID:19772383

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  Triangle network motifs predict complexes by complementing high-error interactomes with structural information. PMID:19558694

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  MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. PMID:19443443

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  NNcon: improved protein contact map prediction using 2D-recursive neural networks. PMID:19420062

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  Computational study of the heterodimerization between mu and delta receptors. PMID:19214754

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  VASCo: computation and visualization of annotated protein surface contacts. PMID:19166624

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  POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. PMID:19091689

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  Coevolution in defining the functional specificity. PMID:18831050

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  Protein co-evolution, co-adaptation and interactions. PMID:18818697

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  Predicting and validating protein interactions using network structure. PMID:18654616

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  Multiple sequence alignments as tools for protein structure and function prediction. PMID:18629077

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  Interactome data and databases: different types of protein interaction. PMID:18629062

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  Prediction of enzyme function by combining sequence similarity and protein interactions. PMID:18505562

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  Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein-protein interaction dataset. PMID:18281313

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  Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. PMID:18277381

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  Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context. PMID:17955155

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  False positive reduction in protein-protein interaction predictions using gene ontology annotations. PMID:17645798

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  High-throughput identification of interacting protein-protein binding sites. PMID:17594507

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  Improved residue contact prediction using support vector machines and a large feature set. PMID:17407573

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  Predicting protein-protein interactions based only on sequences information. PMID:17360525

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  Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology. PMID:17254302

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  SPIDer: Saccharomyces protein-protein interaction database. PMID:17254300

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  Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. PMID:17109752

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  STRING 7--recent developments in the integration and prediction of protein interactions. PMID:17098935

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  Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. PMID:16641319

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  Computational approaches for predicting protein-protein interactions: a survey. PMID:16548413

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  Two-component signal transduction systems of Desulfovibrio vulgaris: structural and phylogenetic analysis and deduction of putative cognate pairs. PMID:16547644

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  Determination of network of residues that regulate allostery in protein families using sequence analysis. PMID:16434743

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  Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. PMID:16398927

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  Oligomeric protein structure networks: insights into protein-protein interactions. PMID:16336694

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  Insights into the quaternary association of proteins through structure graphs: a case study of lectins. PMID:16173917

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  Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. PMID:16087736

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  Assessing the limits of genomic data integration for predicting protein networks. PMID:15998909

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  Stationary cell size distributions and mean protein chain length distributions of Archaea, Bacteria and Eukaryotes described with an increment model in terms of irreversible thermodynamics. PMID:15986097

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  Context dependence and coevolution among amino acid residues in proteins. PMID:15865995

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  Assessing predictions of protein-protein interaction: the CAPRI experiment. PMID:15659362

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  When monomers are preferred: a strategy for the identification and disruption of weakly oligomerized proteins. PMID:15642257

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  Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. PMID:15606919

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  In different organisms, the mode of interaction between two signaling proteins is not necessarily conserved. PMID:15289606

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  Computational approaches to protein-protein interaction. PMID:15185965

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  TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. PMID:14724320

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  From gene networks to gene function. PMID:14656964

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  HPr kinase/phosphorylase, the sensor enzyme of catabolite repression in Gram-positive bacteria: structural aspects of the enzyme and the complex with its protein substrate. PMID:12837773

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  Development of unified statistical potentials describing protein-protein interactions. PMID:12609891

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More detailed information about this field from each metasource. ×

metabolic and signaling pathways

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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protein-protein interactions

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

---

protein interactions

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:42.839615

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metabolic and signaling pathways protein-protein interactions protein interaction