• MCODE

  • Referenced in 45 articles [sw35748]
  • finding molecular complexes in large protein interaction networks. Results: This paper describes a novel ... densely connected regions in large protein-protein interaction networks that may represent molecular...
  • InterViewer

  • Referenced in 28 articles [sw00443]
  • InterViewer: Dynamic visualization of protein-protein interactions From the perspective of graph drawing ... protein interaction network is challenging because it is a complicated, nonplanar graph with ... system for drawing and exploring protein-protein interaction networks in three-dimensional space...
  • Cytoscape

  • Referenced in 69 articles [sw09080]
  • databases of protein-protein, protein-DNA, and genetic interactions that are increasingly...
  • STRING

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

  • Referenced in 26 articles [sw22413]
  • ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties ... proteins. Many important functions of cell are carried out through the proteins therein ... Proteins rarely function alone. Most of their functions essential to life ... associated with various types of protein-protein interactions (PPIs). Therefore, knowledge of PPIs...
  • E-CELL

  • Referenced in 22 articles [sw07917]
  • define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation...
  • iPPBS-Opt

  • Referenced in 16 articles [sw22428]
  • Imbalanced Training Datasets. Knowledge of protein-protein interactions and their binding sites ... living cells. With the avalanche of protein sequences generated in the postgenomic ... identifying in a timely fashion the protein-protein binding sites (PPBSs) based...
  • iHSP-PseRAAAC

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

  • Referenced in 6 articles [sw26869]
  • PIPE: a protein-protein interaction prediction engine based on the re-occurring short ... biochemical approaches used to detect protein-protein interactions are all time and labour ... implementation of a novel Protein-Protein Interaction Prediction Engine termed PIPE. This tool ... capable of predicting protein-protein interactions for any target pair of the yeast...
  • QPath

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

  • Referenced in 9 articles [sw27665]
  • iPPI-PseAAC(CGR): Identify protein-protein interactions by incorporating chaos game representation into...
  • IntelliGEN

  • Referenced in 5 articles [sw01545]
  • distributed workflow system for discovering protein-protein interactions A large genomics project involves ... laboratory is the discovery of protein-protein interactions of fungi, specifically Neurosporacrassa ... larger workflow to discover protein-protein interactions. Novel features of our system include...
  • HIPPIE

  • Referenced in 5 articles [sw29288]
  • function is often modulated by protein-protein interactions (PPIs) and therefore defining ... particular proteins. In many analyses the reliability of the characterization of the interactions becomes ... generated HIPPIE (Human Integrated Protein-Protein Interaction rEference), a human PPI dataset with...
  • DeepPPI

  • Referenced in 4 articles [sw30745]
  • DeepPPI: Boosting Prediction of Protein-Protein Interactions with Deep Neural Networks. The complex ... 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 ... DeepPPI (Deep neural networks for Protein-Protein Interactions prediction), which employs deep neural...
  • APBS

  • Referenced in 87 articles [sw05766]
  • most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media ... diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit...
  • NeMoFinder

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

  • Referenced in 5 articles [sw27666]
  • protein degradation and protein-protein interactions. Experimental studies have revealed that signalling...
  • meta-PPISP

  • Referenced in 3 articles [sw22473]
  • meta web server for protein-protein interaction site prediction. A number of complementary ... have been developed for predicting protein-protein interaction sites. We sought to increase...
  • NOXclass

  • Referenced in 3 articles [sw35408]
  • NOXclass: prediction of protein-protein interaction types. Results: Six interface properties have been ... classification of these three types of interactions using a leave-one-out cross-validation procedure ... hypotheses regarding the nature of protein-protein interactions, when experimental results...
  • PPI_SVM

  • Referenced in 2 articles [sw30744]
  • Prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency ... tables. Protein-protein interactions (PPI) control most of the biological processes ... functions, a knowledge of protein-protein interactions is necessary. Prediction...