This category contains links to useful resources for protein sequence and structure analyses. Resources for phylogenetic analyses, prediction of protein features, and analyses of interactions are also found here.
This sections contains links to several programs which predict protein secondary structure. A link to resources for the evaluation of protein structure prediction is also found here.
This section includes tools for searching for structural motifs, biochemical features found in protein structures, and functional sub-structures such as binding sites.
Resources for the comparison of sequences at the level of tertiary structure are also found here. This includes tools for superimposing structures and for creating structural alignments.
This section contains links to resources to aid in protein 3D structure prediction.
Links to tools for visualization of 3D structures are found here. This section also contains links to many 3D structure databases.
This section contains links to tools for annotating proteins and predicting protein function, localization, and other classifications.
The resources in this section include protein identification tools as well as tools which can give you information on the chemical structures and amino acid properties of peptide sequences.
This section contains databases of protein sequences, properties, targeting, motifs, domains, structures, and protein families.
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.
This section includes links to tools which can give information about protein domains and/or predict motifs, domains, and patterns in peptide sequences.
You can find links to several good tools for manipulating the appearance and format of protein sequences, collections of protein sequences, and alignments in this section. Protein identification mapping tools are also located here.
This section contains links to tools related to predicting subcellular localization, the presence of transmembrane regions, and/or targeting including the prediction of signal peptides.
This section includes resources for molecular dynamics including tools that can predict the movements of structures and/or conformational changes. Molecular docking servers are also included here.
These links include tools and resources for enzyme, metabolic and proteomic pathways and networks. Many of these resources contain dynamic pathway diagrams. Protein-protein interactions are also represented here.
This section contains links to tools and databases for phylogeny reconstruction, including taxonomy resources
This section contains links to protein expression data and resources for analysis of data including 2D gels.
This section contains links to general proteomics resources, methods, software, and databases. Includes mass spectrometry tools.
The links from this subcategory have been moved. They are now located in Top : Sequence Comparison.
These are the sites to visit to find the sequence and/or structure records for your protein of interest.
This section includes links to tools which can predict primary sequence features for the residues of a protein.
These resources include links to protein sequence retrieval tools including BLAST, EMBOSS, Entrez, and SRS.
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