• MCODE

  • Referenced in 43 articles [sw35748]
  • finding molecular complexes in large protein interaction networks. Results: This paper describes a novel ... connected regions in large protein-protein interaction networks that may represent molecular complexes...
  • InterViewer

  • Referenced in 28 articles [sw00443]
  • protein-protein interactions From the perspective of graph drawing, a protein interaction ... network is challenging because it is a complicated, nonplanar graph with a large number ... drawing and exploring protein-protein interaction networks in three-dimensional space. Unique features...
  • STRING

  • Referenced in 26 articles [sw23938]
  • STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Complete knowledge...
  • QPath

  • Referenced in 11 articles [sw35403]
  • querying pathways in a protein-protein interaction network. Results: We present a comprehensive...
  • Cytoscape

  • Referenced in 69 articles [sw09080]
  • source software project for integrating biomolecular interaction networks with high-throughput expression data and other ... databases of protein-protein, protein-DNA, and genetic interactions that are increasingly ... basic functionality to layout and query the network; to visually integrate the network with expression...
  • DeepPPI

  • Referenced in 4 articles [sw30745]
  • Boosting Prediction of Protein-Protein Interactions with Deep Neural Networks. The complex language ... understood. Despite the importance suggested by many proteins variants statistically associated with human disease ... have unknown mechanisms, for example, protein-protein interactions (PPIs). In this study ... called DeepPPI (Deep neural networks for Protein-Protein Interactions prediction), which employs deep...
  • NeMoFinder

  • Referenced in 4 articles [sw29732]
  • NeMofinder: genome-wide protein-protein interactions with meso-scale network motifs. Recent works ... networks such as the protein-protein interaction (PPI) networks. However, existing motif mining...
  • GraMoFoNe

  • Referenced in 3 articles [sw34237]
  • open-source software platform for network visualization and analysis, which supports the development of external ... user, into a Protein-Protein Interaction network previously loaded into the Cytoscape workspace...
  • NatalieQ

  • Referenced in 1 article [sw34156]
  • server for protein-protein interaction network querying. Background: Molecular interactions need ... biological systems. These interactions are captured by various types of biological networks, such as metabolic ... regulatory, signal transduction and protein-protein interaction networks. We recently developed natalie, which ... specified query protein-protein interaction network to a selected target network using...
  • GEDEVO

  • Referenced in 2 articles [sw08298]
  • kinds of biological entities. The emerging interaction networks are usually modeled as graphs with thousands ... biological networks has proven great potential to infer the biological function of proteins and genes. However, the corresponding network alignment problem is computationally hard and theoretically intractable ... protein-protein interaction networks from different organisms we demonstrate that GEDEVO outperforms...
  • iPPBS-Opt

  • Referenced in 16 articles [sw22428]
  • Imbalanced Training Datasets. Knowledge of protein-protein interactions and their binding sites ... indispensable for in-depth understanding of the networks in living cells. With the avalanche ... protein sequences generated in the postgenomic age, it is critical to develop computational methods ... identifying in a timely fashion the protein-protein binding sites (PPBSs) based...
  • dmGWAS

  • Referenced in 3 articles [sw29291]
  • association studies in proteinprotein interaction networks. MOTIVATION: An important question that ... hold promise for comprehensively examining the interactions between genes underlying the pathogenesis of complex diseases ... datasets into the human protein-protein interaction (PPI) network. The DMS method extensively...
  • PIPE

  • Referenced in 6 articles [sw26869]
  • PIPE: a protein-protein interaction prediction engine based on the re-occurring short ... between known interacting protein pairs. Background: Identification of protein interaction networks has received ... biochemical approaches used to detect protein-protein interactions are all time and labour...
  • DyNetViewer

  • Referenced in 1 article [sw24787]
  • construction, analysis and visualization. SUMMARY: The molecular interactions in a cell are varying with time ... construction and analysis of dynamic molecular networks can elucidate dynamic cellular mechanisms of different biological ... visualization of dynamic protein-protein interaction networks. The current version of DyNetViewer consists...
  • NetworkBLAST

  • Referenced in 1 article [sw34157]
  • networks. Summary: The identification of protein complexes is a fundamental challenge in interpreting proteinprotein interaction data. Cross-species analysis allows coping with the high levels ... protein complexes in protein-protein interaction networks. It can analyze a single...
  • HIPPIE

  • Referenced in 5 articles [sw29288]
  • Interaction Networks with Experiment Based Quality Scores. Protein function is often modulated by protein-protein interactions (PPIs) and therefore defining the partners of a protein helps ... generated HIPPIE (Human Integrated Protein-Protein Interaction rEference), a human PPI dataset with ... cbdm.mdc-berlin.de/tools/hippie) allows researchers to do network analyses focused on likely true PPI sets...
  • iPPI-PseAAC

  • Referenced in 9 articles [sw27665]
  • iPPI-PseAAC(CGR): Identify protein-protein interactions by incorporating chaos game representation into ... PseAAC. Investigation into the network of proteinprotein interactions (PPIs) will provide valuable...
  • NABEECO

  • Referenced in 1 article [sw08321]
  • correspondence between nodes from two input networks without using any external knowledge, such as sequence ... editing cost. Applied to Protein-Protein Interaction (PPI) networks, Network Alignment, finds...
  • ProtNet

  • Referenced in 1 article [sw29365]
  • protein interaction networks dynamics. Background: Protein interactions support cell organization and mediate ... data are usually presented as graphs where proteins (nodes) are linked by edges ... This representation reveals that protein-protein interaction (PPI) networks, like other kinds...
  • HPAM

  • Referenced in 3 articles [sw10931]
  • determined by protein-protein interactions among regulatory proteins and with RNA polymerase ... protein-DNA interactions of these trans-acting factors with cis-acting DNA sequences ... regulated genes. Therefore, identifying these protein-DNA interactions, by means of the DNA motifs ... they are connected to build genetic networks. We propose a hybrid promoter analysis methodology (HPAM...