Directory of Protein Analysis Resources

Home > Science > Biology > Bioinformatics > Online Services > Protein Analysis

Online services which provide some sort of analysis of protein structure or sequence.

Subcategories

• Protein Databases

Resources in This Category

• 3D-PSSM Fold Recognition

  http://www.sbg.bio.ic.ac.uk/~3dpssm/
  Combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyond PSI-Blast.

• ConSurf

  http://consurf.tau.ac.il/overview.html
  Identifies functionally important regions on the surface of a protein or domain, of known three-dimensional (3D) structure using the phylogenetic relations between close sequence homologues.

• DisEMBL

  http://dis.embl.de/
  Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein.

• ELM - Functional Sites in Proteins

  http://elm.eu.org/
  Predicts functional sites (linear motifs) in proteins, such as post-translational modification sites, ligand motifs, and targeting signals. Context-based rules and logical filters are applied to improve predictions.

• EpiC

  http://epic.embl.de/
  Resource for the prediction of antigenicity combined with functional analysis of the target protein.

• ESyPred3D

  http://www.fundp.ac.be/urbm/bioinfo/esypred/
  ESyPred3D is an automated homology modeling program getting benefit of the increased alignment performances of a new alignment strategy using neural networks. The final three dimensional structure is built using the modeling package MODELLER.

• InterPro

  http://www.ebi.ac.uk/interpro/
  A database built from Pfam, PRINTS and PROSITE.

• Isoelectric Point Estimator

  http://isoelectric.ovh.org/files/qt4-program-isoelectric.html
  Calculator with graphical user interface written in Qt library.

• JAligner

  http://jaligner.sourceforge.net/
  Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.

• Jpred

  http://www.compbio.dundee.ac.uk/~www-jpred/
  Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED.

• Melanie II 2-D Analysis Software

  http://au.expasy.org/melanie/
  Powerful, state-of-the-art, 2-D analysis software package with user-friendly interface from the Swiss Institute of Bioinformatics.

• MODBASE

  http://salilab.org/modbase
  A database of annotated comparative protein structure models. The database includes fold assignments and alignments as well as information about putative ligand binding sites, SNP annotation, and protein-protein interactions.

• Molecular Biology Tools Online

  http://mbt.biobitfield.com/
  Includes WebOligoMelt (Annealing temperature of oligonucleotides), Virtual Ribosome (translate nucleotide sequences into peptides), and SeqScanGraph (graph melting temperature along nucleotide chain).

• MultiProt

  http://bioinfo3d.cs.tau.ac.il/MultiProt/
  Service for detecting the multiple structural alignments of proteins. Uses the common geometrical cores between the input molecules. Does not require that all the input molecules participate in the alignment.

• Munich Information Center for Protein Sequences (MIPS)

  http://mips.gsf.de/
  Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases.

• PDBeMotif

  http://www.ebi.ac.uk/pdbe-site/pdbemotif/
  Integrated resource, which provides information about ligands, sequence and structure motifs, their relative position and the neighbour environment.

• PFP: Automated Function Prediction Server

  http://dragon.bio.purdue.edu/pfp/
  Accepts a single query protein sequence and returns the most probable Gene Ontology functional annotations in each of the three ontologies.

• Phyre- Protein Homology/analogY Recognition Engine

  http://www.sbg.bio.ic.ac.uk/phyre/
  Phyre is a free for academics service for predicting the 3-dimensional structure of a protein amino acid sequence.

• ProPred-I

  http://www.imtech.res.in/raghava/propred1
  An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results.

• Protein Information Resource

  http://pir.georgetown.edu/
  PIR is a non-redundant annotated protein sequence database, and analytical tools, maintained by collaboration of MIPS, in Munich and the Japanese International Protein Sequence Database (JIPID).

• Protein Structure Prediction Server (PSIPRED)

  http://bioinf.cs.ucl.ac.uk/psipred/
  3D protein structure prediction from amino acid sequence. Includes MEMSAT for transmembrane topology prediction, GenTHREADER and mGenTHREADER for fold recognition.

• Proteomics Tools

  http://www.expasy.org/tools/
  Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).

• ProtFun

  http://www.cbs.dtu.dk/services/ProtFun/
  Ab initio predictions of protein function from protein sequence. The method works by integrating various predicted post-translational and localizational aspects of the proteins submitted.

• Protonet

  http://www.protonet.cs.huji.ac.il/
  Provides automatic hierarchical classification of proteins sequences.

• Scansite

  http://scansite.mit.edu/
  Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

• SSM

  http://www.ebi.ac.uk/msd-srv/ssm
  Provides interactive service for matching protein structures in 3D and looking for structural homologues in PDB and SCOP databases, as well as in user-uploaded sets of structures.

• SWISS-PROT + TrEMBL

  http://www.ebi.ac.uk/swissprot/
  The SWISS-PROT database contains high-quality annotation, is non-redundant and cross-referenced to many other databases. SWISS-PROT is accompanied by TrEMBL, a computer-annotated supplement, which contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database, which are not yet integrated into SWISS-PROT.

• The ProCKSI Server

  http://www.procksi.net/
  A decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results.

• TopMatch: Protein Structure Comparison

  http://topmatch.services.came.sbg.ac.at/
  Public web service for the alignment and superposition of protein structures and the instant visualization of structural similarities.

• TRANSFAC-The Transcription Factor Database

  http://www.gene-regulation.com/pub/databases.html#transfac
  A compilation of transcriptional regulatory protein factors and their cognate gene promoter elements along with DNA sequence search and analysis programs - from GBF, Braunschweig, Germany.

• UniProt

  http://www.pir.uniprot.org/
  UniProt (Universal Protein Resource) is a catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.

 

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