National Institutes of Biomedical Innovation, Health and Nutrition
Institute for Protein Research

Bioinformatics Tools

  • CLINE (Comparison of bioLogIcal deNdrogram structurEs), is a web-tool specifically designed for the visual comparison of dendrograms, with an emphasis on the display of matching clusters that, even when not isomorphic, can be perceived as having the same biological meaning.
  • Detail information is here (internal link).
  • PPiPP predicts pair-wise binding sites between two proteins from their amino-acid sequence, using previously trained neural network ensembles. Pairwise prediction strategy also improves the accuracy of binding site predictions in single proteins in the specific context of a known binding protein partner. These partner-aware binding site predictions are also provided in the server output. This method has been extensively benchmarked and shown to outperform partner-blind predictions of interacting residues in proteins. Read the full paper here
  • PSOPIA is an AODE for predicting protein-protein interactions using three seqeucne based features; (I) sequence similarities to a known interacting protein pair, (II) statistical propensities of domain pairs observed in interacting proteins and (III) a sum of edge weights along the shortest path between homologous proteins in a PPI network.
  • Toxygates is an interactive toxicity analysis platform for the data released by The Toxicogenomics Project, Japan. For more details, see the original publication.
  • Sagace - Search for Biomedical Data
  • Sagace is a web-based search engine to discover and retrieve information from biomedical databases in Japan, primarily for biomedial research and drug development.
  • Here we introduce how to use MultiCoMP. The aim of this web application is to help explore multiple conformations of membrane proteins. You can get information about distinct conformations of your protein of interest, visualize the superimposed atomic coordinates and more.
  • HTM-ONE is a neural network-based server to predict multiple properties of helical membrane proteins in an integrated manner. This can identify membrane-spanning regions, lipi-accessible residues, dihedral angles and several other properties. For helical membrane proteins of known structures, this server is useful to identify unusual geometries which are indicative of flexibility or other functional associations. Read full paper here
  • TargetMine is an integrated data warehouse for retrieval of target genes and proteins for experimental characterisation and drug discovery.
  • It utilises a customised InterMine framework, which enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data.
  • TargetMine also facilitates analysis of query gene/protein sets for enriched biological themes and associations, which can be employed for candidate gene prioritisation.
  • PSIVER (Protein-protein interaction SItes prediction serVER)a server for predicting protein-protein interation sites in protein seqeunces, using only sequence features (position specific scoring matrix and predicted accessibility) and using a Naive Bayes classifier (NBC) and a kernel density estimation method (KDE). This server is free and open to all users and there is no login requirement.
  • Useful Links: Overview
  • SDC PRED - Specific DNA Contact Prediction
  • This tool can predict specific DNA-contacts in proteins, using sequence or structure information.
  • This web server predicts the mononucleotide and dinucleotide base step contacts in protein using evolutionary information in the form of PSSM using Neural Networks. The input is an amino acid sequence in the fasta format.

FUGUE - Protein structure prediction using remote homology detection

  • FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure. Given a query sequence (or a sequence alignment), FUGUE scans a database of structural profiles, calculates the sequence-structure compatibility scores and produces a list of potential homologues and alignments.
  • Useful Links:
  • Documentation
  • Fugue homology search server
  • Fugue alignment server
  • Download Fugue

CBS Pred ? Carbohydrate binding site prediction:

  • Prediction of carbohydrate-binding sites from sequence and PSSM, using NN.
  • Carbohydrate binding site prediction.
  • Prediction of carbohydrate-binding sites from sequence and PSSM, using NN.

HOMSTRAD - A database of structure-based alignments for protein families

  • HOMSTRAD (HOMologous STRucture Alignment Database) is a curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER. These structure-based alignments are annotated with JOY and examined individually.
  • Useful Links:



JOY - Structural annotations and formatting for protein sequences and alignments

  • JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and help understand the conservation of amino acids in their specific local environments. For instance, it has been recognised that a sidechain hydrogen-bonded to a main-chain amide plays an important role in stabilizing the 3D structure and is generally well conserved during evolution. Such a residue is shown in a bold-face letter in the formatted alignments. Another example is the importance of solvent inaccessible residues which are shown in UPPER-CASE letters.
  • Useful Links: