> > Do-it-all Tools for Protein

Do-it-all Tools for Protein

These resources are free, publicly available, multi-purpose tools for protein sequence analysis. This is a good place to start if you're looking for a general sequence analysis package.

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Found 15 links

Displaying 15 links

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

BCM Search LauncherResource Content

http://searchlauncher.bcm.tmc.edu/

DNA > DNA and Genomic Analysis
Protein > Do-it-all Tools for Protein

Molecular biology-related search and analysis services organized by function; single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters).

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tagsanimals database management systems factual databases humans molecular biology

Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/

DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Localization and Targeting
Protein > Molecular Dynamics and Docking
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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eBioinformaticsResource Content

http://www.ebioinformatics.org/

DNA > DNA and Genomic Analysis
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Presentation and Format
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

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EMBOSSTool Content

http://emboss.bioinformatics.nl/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Presentation and Format
Protein > Sequence Features
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.

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tagsmolecular biology sequence alignment

ExPASy Molecular Biology ServerResource Content

http://www.expasy.org/

Education > Directories and Portals
Protein > Do-it-all Tools for Protein

Expert Protein Analysis System; programs and databases for the analysis of protein sequences, structures and 2-D PAGE.

NAR Web Server Issue 2003
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tagsenzymes gel electrophoresis molecular models protein conformation protein databases protein sequence analysis proteins proteomics systems integration

IEDB-ARTool Content

http://tools.immuneepitope.org

Human Genome > Health and Disease
Protein > Do-it-all Tools for Protein

The Immune Epitope Database Analysis Resource (IEDB-AR) is a collection of tools for the prediction and analysis of immune epitopes. Tools include B-cell and T-cell epitope prediction and epitope analysis tools.

NAR Web Server Issue 2008
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tagsb-lymphocyte epitopes factual databases histocompatibility antigens class i histocompatibility antigens class ii peptides proteins t-lymphocyte epitopes

MassNetTool Content

http://massnet.kr

Protein > Do-it-all Tools for Protein
Protein > Proteomics

MassNet web server provides comprehensive functional annotation of mass spectrometry data. Annotation includes physico-chemical analysis, KEGG pathway assignment, GO mapping, and protein-protein interaction prediction.

NAR Web Server Issue 2008
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tagsmass spectrometry protein databases protein interaction mapping proteins

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

NAR Web Server Issue 2006
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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

NRSASTool Content

http://www.receptors.org/NR/servers/html/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.

NAR Web Server Issue 2003
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tagscytoplasmic and nuclear receptors hormones hydrogen bonding molecular models mutation protein conformation protein structural homology

Phylogeny.frTool Content

http://www.phylogeny.fr/

Protein > Do-it-all Tools for Protein
Protein > Phylogeny Reconstruction

Phylogeny.fr is a seamless automation of the various components in pylogenetic analyses from identification of homologous sequences, construction of multiple alignments, phylogenetic reconstruction to graphical representation of the inferred phylogenetic tree.

NAR Web Server Issue 2008
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tagsdna sequence analysis phylogeny protein sequence analysis sequence alignment

PROTEUS2Tool Content

http://wishart.biology.ualberta.ca/proteus2

Protein > Do-it-all Tools for Protein

PROTEUS2 is a web server for comprehensive protein structure prediction and structure-based annotation. The analysis pipeline includes signal identification, trans-membrane helix prediction, trans-membrane beta-strand prediction, secondary structure prediction and homology modeling for user inputs of single or multiple sequences.

NAR Web Server Issue 2008
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tagsalgorithms membrane proteins molecular models protein sequence analysis protein sorting signals protein structural homology secondary protein structure

SeWeRTool Content

http://bioinformatics.org/sewer/

DNA > DNA and Genomic Analysis
Protein > Do-it-all Tools for Protein

Sequence analysis tools on the web; includes nucleic acid, protein, PCR and alignment tools.

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tagscomputational biology database management systems information services

TarOTool Content

http://www.compbio.dundee.ac.uk/taro

Protein > Do-it-all Tools for Protein

TarO is a collection of tools for protein target optimization analysis. Tools include those for annotation of putative orthologues and homologues, searches against the PDB with PSIBLAST, generation of annotated multiple sequence alignments and presentation of integrated results.

NAR Web Server Issue 2008
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tagsalgorithms amino acid sequence homology protein databases protein sequence analysis proteins sequence alignment tertiary protein structure

UGENETool Content

http://ugene.unipro.ru/

DNA > Tools For the Bench
Protein > Do-it-all Tools for Protein

UGENE is an integrated bioinformatics tool that aims to integrate popular bioinformatics tools and algorithms within a single visual interface that can be easily used by molecular biologists.

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Tags associated with subcategory 'Protein/Do-it-all Tools for Protein'

protein sequence analysis proteins molecular models sequence alignment protein conformation protein structural homology protein databases histocompatibility antigens class i tertiary protein structure phylogeny amino acid sequence homology protein interaction mapping histocompatibility antigens class ii peptides proteomics mutation systems integration hydrogen bonding t-lymphocyte epitopes information services secondary protein structure protein sorting signals cytoplasmic and nuclear receptors hormones enzymes ligands b-lymphocyte epitopes animals mass spectrometry dna sequence analysis algorithms gel electrophoresis computational biology protein kinases transcription factors membrane proteins protein folding phosphoprotein phosphatases database management systems factual databases humans molecular biology