• Memtype-2L

  • Referenced in 39 articles [sw16472]
  • membrane; if it is a membrane protein, the process will be automatically continued with ... incorporating the evolution information through representing the protein samples with the Pse-PSSM (Pseudo Position...
  • UniProt

  • Referenced in 131 articles [sw21320]
  • information. UniProt is an important collection of protein sequences and their annotations, which has doubled ... UniProt to represent the relative amount of knowledge known about each protein. These scores will...
  • 2D-MH

  • Referenced in 21 articles [sw19727]
  • server for generating graphic representation of protein sequences based on the physicochemical properties of their ... called “2D-MH”, is proposed to represent protein sequences. It is formed by incorporating...
  • PseAAC

  • Referenced in 30 articles [sw16469]
  • pseudo amino acid (PseAA) composition can represent a protein sequence in a discrete model without...
  • MCODE

  • Referenced in 48 articles [sw35748]
  • regions in large protein-protein interaction networks that may represent molecular complexes. The method ... outward traversal from a locally dense seed protein to isolate the dense regions according...
  • PseAAC-General

  • Referenced in 16 articles [sw22430]
  • pseudo-amino acid composition for large-scale protein datasets. The general form pseudo-amino acid ... PseAAC) has been widely used to represent protein sequences in predicting protein structural and functional...
  • GPCR-CA

  • Referenced in 35 articles [sw25949]
  • hidden in piles of long and complicated protein sequences. Meanwhile, the gray-level co-occurrence ... images are used to represent the samples of proteins through their pseudo amino acid composition...
  • TM-align

  • Referenced in 14 articles [sw22248]
  • identify the best structural alignment between protein pairs that combines the TM-score rotation matrix ... structure comparison of 10 515 representative protein chains from the Protein Data Bank (PDB) with...
  • STRING

  • Referenced in 30 articles [sw23938]
  • indirect interactions between proteins in a given cell would represent an important milestone towards ... certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various...
  • SubMito-PSPCP

  • Referenced in 6 articles [sw22432]
  • developed a new method for predicting protein submitochondrial locations by introducing a new concept: positional ... used only about 100 features to represent protein sequences, which is much simpler than...
  • PDB-REPRDB

  • Referenced in 5 articles [sw26865]
  • REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). Started...
  • AUTO-MUTE

  • Referenced in 9 articles [sw16878]
  • stability changes upon single residue substitutions in proteins with known native structures. Trained models classify ... from 87 to 94%. Attributes representing each mutant protein are based on a computational mutagenesis...
  • GOASVM

  • Referenced in 6 articles [sw22445]
  • pseudo-amino acid composition. Prediction of protein subcellular localization is an important yet challenging problem ... term frequencies and distant homologs to represent a protein in the general form of Chou...
  • SUPERFAMILY

  • Referenced in 5 articles [sw16889]
  • structural and functional annotation for all proteins and genomes. The SUPERFAMILY annotation is based ... collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level...
  • GADDI

  • Referenced in 6 articles [sw18895]
  • biological data can be naturally represented by graphs, e.g., protein interaction networks, gene regulatory networks...
  • LFM-Pro

  • Referenced in 4 articles [sw35378]
  • features are combined into a representative set for the protein family. The utility and success...
  • DIMA

  • Referenced in 4 articles [sw26868]
  • resource--exploring the protein domain network. Conserved domains represent essential building blocks of most known...
  • seqSample

  • Referenced in 1 article [sw31388]
  • select baits for CoIP experiments when protein complex estimation is the main goal. Expanding upon ... classic framework in which nodes represent proteins and edges represent pairwise interactions, we define generalized ... scheme maintains user-specified quality thresholds for protein complex estimates and, relative to simple random...
  • CFinder

  • Referenced in 25 articles [sw12379]
  • often referred to as modules. In a protein assocation network modules appear as groups ... their own, in which nodes (links) represent the modules (overlaps). We introduce CFinder, a fast ... these groups. We show that in gene (protein) association networks CFinder can be used...
  • RVMAB

  • Referenced in 1 article [sw24037]
  • feature extraction method is employed to represent protein sequences on a Position Specific Scoring Matrix...