• Phobius

  • Referenced in 14 articles [sw27723]
  • Phobius: A combined transmembrane topology and signal peptide predictor. This server is for prediction ... transmembrane topology and signal peptides from the amino acid sequence of a protein...
  • PSIPRED

  • Referenced in 15 articles [sw11340]
  • version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based...
  • HMMTOP

  • Referenced in 7 articles [sw16868]
  • HMMTOP transmembrane topology prediction server. Summary: The HMMTOP transmembrane topology prediction server predicts both ... helical transmembrane segments and the topology of transmembrane proteins. Recently, several improvements have been introduced...
  • OCTOPUS

  • Referenced in 3 articles [sw35319]
  • scores and an extended topological grammar. Motivation: As α-helical transmembrane proteins constitute roughly ... OCTOPUS, a new method for predicting transmembrane protein topology is presented and benchmarked using ... modeling of reentrant/membrane-dipping regions and transmembrane hairpins in the topological grammar. Availability: OCTOPUS is available...
  • PSOFuzzySVM-TMH

  • Referenced in 3 articles [sw27664]
  • PSOFuzzySVM-TMH: identification of transmembrane helix segments using ensemble feature space by incorporated fuzzy support ... survival of organisms. The topology of transmembrane proteins describes the number of transmembrane (TM) helix ... identification of TM helix and its topology through experimental methods is laborious with low throughput ... letter exchange group are used to formulate transmembrane protein sequences. The noisy and extraneous attributes...
  • PRED-TMBB

  • Referenced in 5 articles [sw11338]
  • TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins ... Hidden Markov Model, capable of predicting the transmembrane beta-strands of the gram-negative bacteria ... thereafter localize the transmembrane strands and find the topology of the loops...
  • IgTM

  • Referenced in 1 article [sw35357]
  • IgTM: An algorithm to predict transmembrane domains and topology in proteins. Background: Due to their ... used Grammatical Inference (GI) to localize transmembrane segments. Our GI process is based specifically ... input sequences. An encoding that includes the topology changes in the sequence (from inside...
  • R

  • Referenced in 10196 articles [sw00771]
  • R is a language and environment for statistical...
  • LIBSVM

  • Referenced in 1204 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • CHARMM

  • Referenced in 120 articles [sw05953]
  • CHARMM (Chemistry at HARvard Macromolecular Mechanics). CHARMM models...
  • Wesseling

  • Referenced in 329 articles [sw09677]
  • A single processor public domain Fortran-77 code...
  • ClustalW

  • Referenced in 138 articles [sw12016]
  • CLUSTAL W: improving the sensitivity of progressive multiple...
  • KEGG

  • Referenced in 281 articles [sw13866]
  • KEGG: Kyoto Encyclopedia of Genes and Genomes. KEGG...
  • PISCES

  • Referenced in 31 articles [sw16873]
  • PISCES: a protein sequence culling server. Summary: PISCES...
  • PHAT

  • Referenced in 3 articles [sw17270]
  • PHAT: A transmembrane-specific substitution matrix. Motivation: Database...
  • BLAST

  • Referenced in 251 articles [sw17334]
  • Basic Local Alignment Search Tool. BLAST finds regions...
  • Pfam

  • Referenced in 105 articles [sw23108]
  • Pfam: clans, web tools and services. Pfam is...
  • AAindex

  • Referenced in 47 articles [sw26861]
  • AAindex: amino acid index database. AAindex is a...