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Protein Sequence & Structure

Protein Sequence & Structure

Physiochemical Properties
  • ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)
  • ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)

Analyse Primary Sequence
  • ProtColourer (Make colour-coded representation of an amino acid sequence at EBI)
  • ProtScale (Hydrophobicity, other conformational parameters, etc. at ExPASy)
  • SignalP (Prediction of peptide signal sequence at CBS, Denmark)
  • TargetP (Prediction of subcellular localization at CBS, Denmark)
  • NetOGlyc (Prediction of O-glycosylation sites in mammalian proteins at CBS, Denmark)
  • NetPhos (Prediction of phosphorylation sites in eukaryotic proteins)
  • Helical Wheel (Representation of alpha-helical peptides)
  • Hydropathy plots (At Pensylvania State University, Department of Biochemistry and Molecular Biology)
  • SAPS (Statistical Analysis for charge clusters, repeats, hydrophobic regions, compositional domains etc. at ISREC, CH)
  • PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
  • DGPI (Prediction of GPI-anchor and cleavage sites, University of Geneva, CH)
  • Scansite (Prediction of protein signaling sequence motifs at HIM, Boston, USA)
  • Other primary sequence analysis tools at ExPaSy
  • Pairwise

  • Blast 2 Sequences (Alignment of two protein sequences using BLAST at NCBI, USA)

  • SIM (Alignment of 2 protein sequences at ExPASy, Switzerland)

  • Pairwise sequence alignment (at Baylor College of Medecine, USA)

  • Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)

  • Multiple

  • ClustalW (at EBI, UK)

  • ClustalW (at the Baylor College of Medicine, USA)

  • MAP (Multiple alignment of (long) sequences without penalizing large gaps)

  • Multiple sequence alignment (at Baylor College of Medecine, USA)

  • Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)

  • AMAS (Analyze multiple aligned sequences at Oxford University, UK)

  • Editors

  • CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)

  • BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)

Predict Secondary Structure
  • TMpred (Prediction of membrane-spanning regions and their orientation at ISREC)
  • SOSUI (Prediction of Transmembrane Regions, JP)
  • DAS (Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method, Stockholm University)
  • TopPred2 (Topology prediction of membrane proteins at the Institut Pasteur, Paris, France)
  • JPred (Protein secondary structure prediction at EBI)
  • HNN (Hierarchical Neural Network secondary structure prediction at NPS, Lyon, France)
  • nnPredict (Protein secondary structure prediction at UCSF, CA, USA)
  • BTPRED (Prediction of beta-turns at UCL, UK)
  • PairCoil (Prediction of coiled Coil regions, Bergers method)
  • TOPS (Protein topology cartoon generation at EBI, UK)
  • TMHMM (Prediction of transmembrane helices in proteins at CBS, Denmark)
  • PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
  • HMMTOP (Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences)
  • PredictProtein (Protein secondary structure prediction at EMBL)
  • Predator (Secondary structure prediction from single or multiple sequences at EMBL, Heidelberg)
  • PSIpred (Protein secondary structure prediction at Brunel University, UK)
  • Other secondary structure prediction tools at ExPASy
  • Coils (Prediction of coiled Coil regions Lupas' method at EMBnet-CH)
  • MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies at WI , USA)
  • TOPS (Protein topology cartoon generation at University of Leeds, UK)


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