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Protein Analysis (45)
Categories:
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Sites:
» 3D-JIGSAW 
Automated comparative (homology) protein modelling, including an interactive mode which highlights known domains and allows users to select and align templates.
http://www.bmm.icnet.uk/~3djigsaw/
Automated comparative (homology) protein modelling, including an interactive mode which highlights known domains and allows users to select and align templates.
http://www.bmm.icnet.uk/~3djigsaw/
» 3D-PSSM Fold Recognition
Combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyond PSI-Blast.
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.
http://www.sbg.bio.ic.ac.uk/~3dpssm/
» BioInfoBank Meta Server
Offers a gateway to well-benchmarked protein structure and function prediction methods. Structural models collected from the predictions servers are assessed using the powerful 3D-jury consensus approach.
http://meta.bioinfo.pl/submit_wizard.pl
Offers a gateway to well-benchmarked protein structure and function prediction methods. Structural models collected from the predictions servers are assessed using the powerful 3D-jury consensus approach.
http://meta.bioinfo.pl/submit_wizard.pl
» COLORADO3D
Service to aid visualisation of potential errors in protein structures. Free for academic users.
http://asia.genesilico.pl/colorado3d/
Service to aid visualisation of potential errors in protein structures. Free for academic users.
http://asia.genesilico.pl/colorado3d/
» Combinatorial Extension of Polypeptides
Method for finding 3-D similarities in protein structures from the UCSD Supercomputer Center.
http://cl.sdsc.edu/ce.html
Method for finding 3-D similarities in protein structures from the UCSD Supercomputer Center.
http://cl.sdsc.edu/ce.html
» ConSurf
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.
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.
http://consurf.tau.ac.il/overview.html
» DisEMBL
Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein.
http://dis.embl.de
Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein.
http://dis.embl.de
» ELM - Functional Sites in Proteins
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.
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.
http://elm.eu.org
» EMBL Bioinformatic Harvester
Collection of human (swall) proteins, crossreferences to major prediction servers. Supported predictions from: smart, string, blast, swall, mapview, sosui, ipsort and ncbi conserved domains.
http://harvester.embl.de
Collection of human (swall) proteins, crossreferences to major prediction servers. Supported predictions from: smart, string, blast, swall, mapview, sosui, ipsort and ncbi conserved domains.
http://harvester.embl.de
» ESyPred3D
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.
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.
http://www.fundp.ac.be/urbm/bioinfo/esypred/
» EpiC
Resource for the prediction of antigenicity combined with functional analysis of the target protein.
http://epic.embl.de
Resource for the prediction of antigenicity combined with functional analysis of the target protein.
http://epic.embl.de
» InterPro - The Integrated Resource of Protein Domains and Functional Sites.
A database built from Pfam, PRINTS and PROSITE.
http://www.ebi.ac.uk/interpro/
A database built from Pfam, PRINTS and PROSITE.
http://www.ebi.ac.uk/interpro/
» Isoelectric Point Estimator
Calculator with graphical user interface written in Qt library.
http://isoelectric.ovh.org/files/qt4-program-isoelectric.html
Calculator with graphical user interface written in Qt library.
http://isoelectric.ovh.org/files/qt4-program-isoelectric.html
» JAligner
Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
http://jaligner.sourceforge.net/
Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
http://jaligner.sourceforge.net/
» Jpred
Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED.
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.
http://www.compbio.dundee.ac.uk/~www-jpred/
» 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.
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.
http://salilab.org/modbase
» Melanie II 2-D Analysis Software
Powerful, state-of-the-art, 2-D analysis software package with user-friendly interface from the Swiss Institute of Bioinformatics.
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.
http://au.expasy.org/melanie/
» Molecular Biology Tools Online
Includes WebOligoMelt (Annealing temperature of oligonucleotides), Virtual Ribosome (translate nucleotide sequences into peptides), and SeqScanGraph (graph melting temperature along nucleotide chain).
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).
http://mbt.biobitfield.com/
» Molecules To Go
Search engine for visualizing 3-D biomolecular models. From the Center for Molecular Modeling, NIH, Maryland.
http://molbio.info.nih.gov/cgi-bin/pdb/
Search engine for visualizing 3-D biomolecular models. From the Center for Molecular Modeling, NIH, Maryland.
http://molbio.info.nih.gov/cgi-bin/pdb/
» 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.
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.
http://bioinfo3d.cs.tau.ac.il/MultiProt/
» Munich Information Center for Protein Sequences (MIPS)
Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases.
http://mips.gsf.de/
Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases.
http://mips.gsf.de/
» PDBeMotif
Integrated resource, which provides information about ligands, sequence and structure motifs, their relative position and the neighbour environment.
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.
http://www.ebi.ac.uk/pdbe-site/pdbemotif/
» PFP: Automated Function Prediction Server
Accepts a single query protein sequence and returns the most probable Gene Ontology functional annotations in each of the three ontologies.
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.
http://dragon.bio.purdue.edu/pfp/
» Phyre- Protein Homology/analogY Recognition Engine
Phyre is a free for academics service for predicting the 3-dimensional structure of a protein amino acid sequence.
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.
http://www.sbg.bio.ic.ac.uk/phyre/
» PredictProtein Server
Most widely used server for analysing protein sequences, searching protein databases, and predicting protein structure - from Columbia Univ.
http://cubic.bioc.columbia.edu/predictprotein/
Most widely used server for analysing protein sequences, searching protein databases, and predicting protein structure - from Columbia Univ.
http://cubic.bioc.columbia.edu/predictprotein/
» ProPred-I
An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results.
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.
http://www.imtech.res.in/raghava/propred1
» 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.
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.
http://www.cbs.dtu.dk/services/ProtFun/
» Protein Information Resource
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).
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).
http://pir.georgetown.edu/
» Protein Structure Prediction Server (PSIPRED)
3D protein structure prediction from amino acid sequence. Includes MEMSAT for transmembrane topology prediction, GenTHREADER and mGenTHREADER for fold recognition.
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.
http://bioinf.cs.ucl.ac.uk/psipred/
» Proteomics Tools
Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).
http://www.expasy.org/tools/
Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).
http://www.expasy.org/tools/
» Protonet
Provides automatic hierarchical classification of proteins sequences.
http://www.protonet.cs.huji.ac.il
Provides automatic hierarchical classification of proteins sequences.
http://www.protonet.cs.huji.ac.il
» Quaternary Structure Prediction
An experimental bioinformatics server. Classifies protein sequences as homodimers or non-homodimers. Applications: metabolic reconstruction, protein structure and function assignment, and drug-design.
http://mericity.com/
An experimental bioinformatics server. Classifies protein sequences as homodimers or non-homodimers. Applications: metabolic reconstruction, protein structure and function assignment, and drug-design.
http://mericity.com/
» 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.
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.
http://www.ebi.ac.uk/msd-srv/ssm
» SWISS-PROT + TrEMBL
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) pr
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) pr
http://www.ebi.ac.uk/swissprot/
» Scansite
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.
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.
http://scansite.mit.edu/
» Swiss-Model
Automated comparative protein modelling server to make protein modelling accessible to biochemists and molecular biologists worldwide - from GlaxoWellcome Experimental Research, Geneva, Switzerland.
http://swissmodel.expasy.org//SWISS-MODEL.html
Automated comparative protein modelling server to make protein modelling accessible to biochemists and molecular biologists worldwide - from GlaxoWellcome Experimental Research, Geneva, Switzerland.
http://swissmodel.expasy.org//SWISS-MODEL.html
» Swiss-Pdb Viewer
User-friendly interface allowing analysis of several proteins at once, including superimposition to deduce structural alignments, and compare active sites. From GlaxoWellcome Experimental Research, Geneva, Switzerland.
http://au.expasy.org/spdbv/
User-friendly interface allowing analysis of several proteins at once, including superimposition to deduce structural alignments, and compare active sites. From GlaxoWellcome Experimental Research, Geneva, Switzerland.
http://au.expasy.org/spdbv/
» TRANSFAC-The Transcription Factor Database
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.
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.
http://www.gene-regulation.com/pub/databases.html#transfac
» The ProCKSI Server: Protein Comparison, Knowledge, Similarity and Information
ProCKSI is a decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results.
http://www.procksi.net
ProCKSI is a decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results.
http://www.procksi.net
» TopMatch: Protein Structure Comparison
Public web service for the alignment and superposition of protein structures and the instant visualization of structural similarities.
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.
http://topmatch.services.came.sbg.ac.at
» UniProt
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.
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.
http://www.pir.uniprot.org/
» Wurst
A protein threading server using sequence profiles combined with a protein sequence to structure compatibility function based on Bayesian statistics.
http://www.zbh.uni-hamburg.de/wurst
A protein threading server using sequence profiles combined with a protein sequence to structure compatibility function based on Bayesian statistics.
http://www.zbh.uni-hamburg.de/wurst
» iMolTalk
Provides protein structure information such as structural alignment, residue contact, protein-protein interfaces, contact maps and general information extraction.
http://i.moltalk.org
Provides protein structure information such as structural alignment, residue contact, protein-protein interfaces, contact maps and general information extraction.
http://i.moltalk.org
» protSPHERE
Tool to organize and analyze BLAST protein-data. It's free to use for scientific purpose.
http://www.protsphere.com
Tool to organize and analyze BLAST protein-data. It's free to use for scientific purpose.
http://www.protsphere.com
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Last Updated: 2010-02-16 15:58:09
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