Home List of Tools Analysis Work Flow Help Lab Page
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NCBS - IWS / List of Tools :

Protein Sequence Search :
  • CASCADE PSI-BLAST
  • SCANMOT - Search for similar sequences using a simultaneous scan of multiple sequence motifs
  • PSI-BLAST search gainst PASS2 Database
  • PHI-BLAST search against PASS2 Database
  • PSI-BLAST Plus : PSI-BLAST results parsed with MView for quick and easy interpretation of the result
  • HMM search against PASS2 Database to identify Structural Templates

    Sequence Alignment :
  • FMALIGN - Multiple Alignment
  • Multiple Sequence Alignment using MALIGN
  • MALIGN Search against PASS2 Database to identify Structural templates
  • Alignment Statistics using ALISTAT
  • Find iMOT(Interacting MOTifs) from an alignment using iMOT Algorithm

    Sequence Analysis :
  • SEQPLOT - Consensus Sequence plotting program based on various amino acid indices
  • Identify Structural Domains from Protein Sequence using DIAL (Domain Identification ALgorithm)
  • Identify Sequentialy conserved regions in Proteins sequence using iMOT Algorithm
  • SEQREPORT - Aminoacid composition, Molecular weight, Molar absorption coefficient, Protein isoelectric point with pK values, Charge at different pH, sequence as 3 letters aminoacid code and Classification of amino acid residues
  • Identify Spatially Interacting Motifs in Proteins sequence using iMOT Algorithm
  • Identify sequence motifs from Protein Sequence using MOTIFS program
  • Identify structural domain architecture using GenDis Tool

    Secondory Structure Prediction:
  • Access Various Secondory Structure Servers through a single Window of NCBS-IWS

    Structure Analysis :
  • SMotif - Structural Motifs in Proteins
  • Identify Structural Domains using DIAL (Domain Identification ALgorithm)
  • Calculate Stabilizing Energy, Hydrophobic Interaction, Salt Bridges, Electrostatic Interaction, and Short Contacts using COILCHECK
  • Calculate mainchain to mainchain hydrogen bonds (amide), Mainchain to mainchain hydrogen bonds (carbonyl), DSSP, positive phi angle, accessibility and Ooi number using JOY Program
  • Secondory Structural Patterns using SSTRUC
  • Calculate C-alpha distance between two atoms of a PDB file
  • Hydrogen bonding Properties using HBOND
  • Extract Sequence Information from a PDB file using atm2seq
  • Generate JOY Structural features output for a PDB File
  • iMOTdb - Database of Spatially Interacting Motifs in Proteins
  • Calculate RMS Deviation between two structures using SUPER
  • Difference Distance Matrix using DDM
  • SMoS (Structural Motifs of Superfamilies) Database - provides information on structural motifs or templates of aligned protein domain superfamilies like PASS2 and CAMPASS
  • Generate MOLSCRIPT Images of Macromolecules

    Protein Modeling & Structure Validation:
  • MODIP (Modeling Of DIsulphide bonds in Proteins )Online
  • Build Proteins using MODELLER
  • Validate Protein Models using HARMONY

    Sequence-Structure Analysis
  • Calculate mainchain to mainchain hydrogen bonds (amide), Mainchain to mainchain hydrogen bonds (carbonyl), DSSP, positive phi angle, accessibility and Ooi number using JOY Program
  • SSToSS - Database of Sequence-Structural Templates of Single-member Superfamilies
    Fold Prediction Tools
  • SCANMOT - Search for similar sequences using a simultaneous scan of multiple sequence motifs
  • FASSM Server: Enhanced Function Association in whole genome analysis using Sequence and Structural Motifs
  • Link Out to Various Fold Prediction Servers


    Phylogenetic Analysis Tools
  • PROTPARS - Estimate phylogenies from protein sequences (PHYLIP)
  • PROTDIST - Computes a distance measure for protein sequences (PHYLIP)
  • PROML - Estimates phylogenies from protein amino acid sequences by maximum likelihood (PHYLIP)
  • PROMLK - Same as PROML but assumes a molecular clock (PHYLIP)
  • SEQBOOT - Reads in a data set, and produces multiple data sets from it by bootstrap resampling (PHYLIP)
  • CONSENSE - Computes consensus trees by the majority-rule consensus tree method (PHYLIP)
  • NEIGHBOR - Neighbor-Joining method of Saitou and Nei (1987) and the UPGMA method of clustering (PHYLIP)
  • KITSCH - Fitch-Margoliash and Least Squares Methods with Evolutionary Clock (PHYLIP)
  • Link Out to Various Phylogenetic Analysis Programs

  • Contact:
    Dr. R. Sowdhamini (mini@ncbs.res.in)
    Shameer Khadar