• MCODE

  • Referenced in 49 articles [sw35748]
  • finding molecular complexes in large protein interaction networks. Results: This paper describes a novel graph ... densely connected regions in large protein-protein interaction networks that may represent molecular complexes ... which is relevant for protein networks. Protein interaction and complex information from the yeast Saccharomyces ... evaluation. Conclusion: Dense regions of protein interaction networks can be found, based solely on connectivity...
  • InterViewer

  • Referenced in 29 articles [sw00443]
  • InterViewer: Dynamic visualization of protein-protein interactions From the perspective of graph drawing, a protein ... system for drawing and exploring protein-protein interaction networks in three-dimensional space. Unique features ... used not only for drawing protein interaction networks but also for simplifying them into different ... provides an integrated framework for querying protein interaction databases and directly visualizing the query results...
  • STRING

  • Referenced in 34 articles [sw23938]
  • STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Complete knowledge ... direct and indirect interactions between proteins in a given cell would represent an important milestone ... model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels ... global view of all the available interaction data is desirable, including lower-quality data and/or computational...
  • IntAct

  • Referenced in 31 articles [sw21665]
  • IntAct:an open source molecular interaction database. IntAct provides an open source database and toolkit ... storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical ... representations of protein interactions, and allows exploring interaction networks in the context ... annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction...
  • Cytoscape

  • Referenced in 80 articles [sw09080]
  • large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available ... interaction pathways correlating with changes in gene expression, a study of protein complexes involved...
  • BioGRID

  • Referenced in 48 articles [sw17422]
  • Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein ... User-customized graphs with embedded protein, gene and interaction attributes can be constructed with...
  • iPPI-Esml

  • Referenced in 26 articles [sw22413]
  • ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet ... associated with various types of protein-protein interactions (PPIs). Therefore, knowledge of PPIs is fundamental ... drug development. With the avalanche of proteins sequences generated in the postgenomic...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression ... computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds...
  • KEGG

  • Referenced in 280 articles [sw13866]
  • molecular building blocks of genes and proteins (genomic information) and chemical substances (chemical information) that ... knowledge on molecular wiring diagrams of interaction, reaction and relation networks (systems information). It also...
  • iDrug-Target

  • Referenced in 13 articles [sw22415]
  • approach. Information about the interactions of drug compounds with proteins in cellular networking is very ... existing predictors for identifying drug-protein interactions were trained by a skewed benchmark data ... where the number of non-interactive drug-protein pairs is overwhelmingly larger than that ... lead to the outcome that many interactive drug-protein pairs might be mispredicted...
  • Gromacs

  • Referenced in 125 articles [sw04128]
  • like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions...
  • PathBLAST

  • Referenced in 9 articles [sw29737]
  • PathBLAST: a tool for alignment of protein interaction networks. PathBLAST is a network alignment ... search tool for comparing protein interaction networks across species to identify protein pathways and complexes ... high-scoring alignments between pairs of protein interaction paths, for which proteins of the first ... allows for functional annotation of protein interaction pathways based on similarity to the network...
  • QPath

  • Referenced in 12 articles [sw35403]
  • querying pathways in a protein-protein interaction network. Results: We present a comprehensive framework ... query proteins, and the reliability of their constituent interactions. We applied QPath to systematically infer ... their function. The growing amounts of protein interactions in public databases underscore the importance...
  • QNet

  • Referenced in 11 articles [sw13845]
  • QNet: A Tool for Querying Protein Interaction Networks. Molecular interaction databases can be used ... QNet searches queries with up to 9 proteins in seconds on current networks, and outperforms ... known yeast complexes against a fly protein interaction network. This comparison points to strong conservation ... importance of our tool in mining protein interaction networks...
  • Memtype-2L

  • Referenced in 39 articles [sw16472]
  • biological function of the query protein and to its interaction process with other molecules...
  • PROFEAT

  • Referenced in 14 articles [sw16924]
  • different structural, functional and interaction profiles. PROFEAT (Protein Features) is a web server for computing ... predicting proteins of functional classes, proteinprotein interactions and MHC-binding peptides. PROFEAT is accessible...
  • iHSP-PseRAAAC

  • Referenced in 16 articles [sw25193]
  • They play essential roles in protein-protein interactions such as folding and assisting...
  • iPPBS-Opt

  • Referenced in 16 articles [sw22428]
  • Imbalanced Training Datasets. Knowledge of protein-protein interactions and their binding sites is indispensable ... living cells. With the avalanche of protein sequences generated in the postgenomic...
  • PIPE

  • Referenced in 6 articles [sw26869]
  • PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences ... between known interacting protein pairs. Background: Identification of protein interaction networks has received considerable attention ... biochemical approaches used to detect protein-protein interactions are all time and labour intensive. Consequently ... implementation of a novel Protein-Protein Interaction Prediction Engine termed PIPE. This tool is capable...
  • propy

  • Referenced in 27 articles [sw22402]
  • predicting structural, functional, expression and interaction profiles of proteins and peptides. To facilitate extensive studies...