Protein Sequence And Structure Analysis Tools - 11 August 2011 - BioInformatics Pakistan
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Protein Sequence And Structure Analysis Tools

Protein sequence and structure analysis tools
  1. Physicochemical properties
    • ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)
    • ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)
  2. Analyse primary sequence
    • ProtColourer (Make colour-coded representation of an amino acid sequence at EBI)
    • ProtScale (Hydrophobicity, other conformational parameters, etc. at ExPASy)
    • SAPS (Statistical Analysis for charge clusters, repeats, hydrophobic regions, compositional domains etc. at ISREC, CH)
    • SignalP (Prediction of peptide signal sequence at CBS, Denmark)
    • TargetP (Prediction of subcellular localization at CBS, Denmark)
    • PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
    • NetOGlyc (Prediction of O-glycosylation sites in mammalian proteins at CBS, Denmark)
    • DGPI (Prediction of GPI-anchor and cleavage sites, University of Geneva, CH)
    • NetPhos (Prediction of phosphorylation sites in eukaryotic proteins at CBS, Denmark )
    • Scansite (Prediction of phosphorylation sites and protein binding sites at MIT, Cambridge, USA)
    • Helical Wheel (Representation of alpha-helical peptides)
    • Other primary sequence analysis tools at ExPaSy
  3. Alignment
    • 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)
      • 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)
  4. Predict secondary structure
    • TMpred (Prediction of membrane-spanning regions and their orientation at ISREC).
    • TMHMM (Prediction of transmembrane helices in proteins at CBS, Denmark)
    • SOSUI (Prediction of Transmembrane Regions, JP)
    • PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
    • DAS (Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method, Stockholm University)
    • HMMTOP (Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences)
    • TopPred2 (Topology prediction of membrane proteins at the Institut Pasteur, Paris, France)
    • PredictProtein (Protein secondary structure prediction at EMBL)
    • JPred (Protein secondary structure prediction at Dundee University, UK)
    • HNN (Hierarchical Neural Network secondary structure prediction at NPS@, Lyon, France)
    • PSIpred (Protein secondary structure prediction at Brunel University, UK)
    • nnPredict (Protein secondary structure prediction at UCSF, CA, USA)
    • Other secondary structure prediction tools at ExPASy
    • BTPRED (Prediction of beta-turns at UCL, UK)
    • Coils (Prediction of coiled Coil regions Lupas' method at EMBnet-CH)
    • PairCoil (Prediction of coiled Coil regions by Berger's method)
    • MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies at WI, USA)
    • TOPS (Protein topology cartoon generation at University of Leeds, UK)
  5. Analyse and model 3D structure
    • 3D viewers
    • 3D analysis
      • TOPS
         (Protein topology cartoon generation at University of Leeds, UK)
      • DOMPLOT
         (Generate schematic diagrams of the structural domain organisation annotated by ligand contacts at University College London, UK)
      • OCA
         (Structure database browser at EBI, UK)
         (Molecular Modeling Database MMDB from ENTREZ at NCBI)
      • PsiPred
         (Sequence profile based fold recognition at Brunel University, UK)
      • Predicting Protein 3D structure based on homologous sequence search
         (EMBL Heidelberg, Germany)
      • 123
         (Fold prediction by aligning (threading) to a (set of) structure(s)
      • LOCK
         (Compare 3D structures of query and target proteins (PDB codes) and visualize superposed 3D structures at Stanford University, USA)
      • CE
         (3-D protein structure comparison and alignment using the combinatorial extension (CE) method at SDSC, USA)
      • DALI
         (Automated Protein Structure Alignment at EBI,UK)
      • LIBRA
         (LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading at NIG, Jp)
      • VAST
         (Structure-structure similarity search at NCBI, US)
      • ASC
         (Analytic Surface Calculation of PDB molecules at IMP, Vienna)
      • MolSurfer (Calculate and navigate protein-protein interfaces at EML
        , Germany)
      • Protein-Protein Interaction Server (UCL, UK)
    • 3D homology modeling
      • CPHmodels
         (Structure prediction by comparative homology modeling at CBS, Denmark)
      • Swiss-Model
         (Automated protein homology-modeling server at ExPASy, Switzerland)
      • 3DCrunch
         (Browse database of modeled Swiss-Prot proteins at ExPASy, Switzerland)
      • FAMS
         (Fully Automated Modeling Service at Kitasato University, JP)
      • 3D-Jigsaw
         (Comparative modeling server at Imperial Cancer Research Fund, London, UK )
      • SDSC1
         (Protein structure homology modeling server at SDSC, USA)
      • Meta PP
         (Collection of structure prediction services at Columbia University, USA)
      • List of comparative modeling tools (at the Rockefeller University, NY, USA)

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