• GPCR-CA

  • Referenced in 35 articles [sw25949]
  • cellular automaton image approach for predicting G-protein-coupled receptor functional classes. Given an uncharacterized ... protein sequence, how can we identify whether it is a G-protein-coupled receptor (GPCR ... hidden in piles of long and complicated protein sequences. Meanwhile, the gray-level co-occurrence ... used to represent the samples of proteins through their pseudo amino acid composition (Chou...
  • BioGRID

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

  • Referenced in 41 articles [sw22407]
  • pseudo components of DNA, RNA, and protein sequences. With the avalanche of biological sequences generated ... biological sample (such as DNA, RNA or protein) with a discrete model or a vector ... possible feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those...
  • MODELLER

  • Referenced in 33 articles [sw27731]
  • MODELLER: A Program for Protein Structure Modeling. MODELLER is used for homology or comparative modeling ... protein three-dimensional structures (1,2). The user provides an alignment of a sequence ... hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints ... including de novo modeling of loops in protein structures, optimization of various models of protein...
  • iLoc-Virus

  • Referenced in 31 articles [sw22417]
  • identifying the subcellular localization of virus proteins with both single and multiple sites ... developed for predicting the subcellular locations of proteins according to their sequence information ... concerned contains both single- and multiple-location proteins. Also, among the existing methods, very ... were developed specialized for dealing with viral proteins, those generated by viruses. Actually, knowledge...
  • PROSITE

  • Referenced in 38 articles [sw17326]
  • various databases dedicated to the identification of protein families and domains, PROSITE is the first ... linked to documentation briefly describing the protein family or domain they are designed to detect ... relationship of PROSITE with the SWISS-PROT protein database allows the evaluation of the sensitivity...
  • STRING

  • Referenced in 33 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 ... certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various ... scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe...
  • 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...
  • Plant-mPLoc

  • Referenced in 27 articles [sw22435]
  • augment the power for predicting plant protein subcellular localization. One of the fundamental goals ... biology is to identify the functions of proteins in various cellular organelles and pathways. Information ... subcellular locations of proteins can provide useful insights for revealing their functions and understanding ... existing methods in predicting plant protein subcellular localization can only cover three or four location...
  • pLoc-mEuk

  • Referenced in 30 articles [sw24440]
  • Predict subcellular localization of multi-label eukaryotic proteins by extracting the key GO information into ... predicting the subcellular localization of eukaryotic proteins, but most of the existing methods have ... systems in which each of the constituent proteins has one and only one location. Actually ... proteins with multiple locations are particularly interesting since they may have some exceptional functions very...
  • PISCES

  • Referenced in 31 articles [sw16873]
  • PISCES: a protein sequence culling server. Summary: PISCES is a public server for culling sets ... protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria ... substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists...
  • pLoc-mPlant

  • Referenced in 27 articles [sw25191]
  • predict subcellular localization of multi-location plant proteins by incorporating the optimal GO information into ... biochemistry is to identify the functions of proteins in the context of compartments that organize ... identification of the subcellular locations of uncharacterized proteins. The current study is focused on plant ... protein subcellular location prediction based on the sequence information alone. Although considerable efforts have been...
  • iPPI-Esml

  • Referenced in 26 articles [sw22413]
  • ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet ... into PseAAC. A cell contains thousands of proteins. Many important functions of cell are carried ... 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 is fundamental...
  • GOLEM

  • Referenced in 52 articles [sw24695]
  • successfully on real-world problems such as protein structure prediction and finite element mesh design...
  • Hum-mPLoc

  • Referenced in 26 articles [sw26862]
  • ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple ... sites. Proteins may simultaneously exist at, or move between, two or more different subcellular locations ... Proteins with multiple locations or dynamic feature of this kind are particularly interesting because they ... discovery. For instance, among the 6408 human protein entries that have experimentally observed subcellular location...
  • pLoc-mAnimal

  • Referenced in 27 articles [sw24438]
  • pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites. Motivation ... growth and reproduction are performed via the protein molecules located at their different organelles ... locations. Facing explosive growth of protein sequences, we are challenged to develop fast and effective ... easy task. Particularly, mounting evidences have indicated proteins have multi-label feature meaning that they...
  • BLAT

  • Referenced in 36 articles [sw16891]
  • genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more ... mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when...
  • pSuc-Lys

  • Referenced in 31 articles [sw16643]
  • pSuc-Lys: predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach ... type of post-translational modifications (PTMs), protein lysine succinylation is important in regulating varieties ... facing a challenging problem: for an uncharacterized protein sequence having many Lys residues therein, which...
  • MEGA

  • Referenced in 35 articles [sw09078]
  • software for evolutionary analysis of DNA and protein sequences. The Molecular Evolutionary Genetics Analysis (MEGA ... evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools...
  • Euk-PLoc

  • Referenced in 24 articles [sw22420]
  • ensemble classifier for large-scale eukaryotic protein subcellular location prediction. With the avalanche of newly ... found protein sequences emerging in the post genomic era, it is highly desirable to develop ... networking. However, predicting subcellular location of eukaryotic proteins is a challenging problem, particularly when unknown ... query proteins do not have significant homology to proteins of known subcellular locations and when...