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PhyloBuilder | Gather homologs -> Align sequences -> Construct trees -> Find subfamilies -> Structure prediction

Human Proteome Explorer v. 2.0.   7 November 2009: 16,387 families; 740,415 Hidden Markov Models (families and subfamilies).

We combine evolutionary/phylogenetic analysis with structure analysis to boost the sensitivity and specificity of protein function prediction. Specialized sections of the library are devoted to particular classes of proteins, such as

• G-protein Coupled Receptors (GPCRs)
• Ion Channels
• Innate Immunity molecules.

This HMM library is included in our Universal Proteome Explorer, which you may want to use instead, for increased coverage of protein families.

This work is funded by grant number R01 HG002769 from the National Human Genome Research Institute of the NIH.

Please cite the following paper in references to this resource: "PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification", Genome Biology 2006, 7:R83

Protein Search

Submit sequences for classification against the HMM library. This library is designed to help biologists do the following:

• Predict molecular function by phylogenomic analysis, using the phylogenetic tree for the family.
• Classify novel sequences to functional subtypes, using the subfamily HMMs for the family.
• Predict specificity positions, using the alignment analysis plots for each family.

Browse Books in our library

Each "book" in the HMM library corresponds roughly to a (whole-chain) protein family or domain, and contains the following data (generally downloadable, in different formats):

• A cluster of homologs, typically from many species
• One or more phylogenetic trees.
• A decomposition of the tree into subtrees, to identify functional subfamilies.
• A multiple sequence alignment for the family, as well as for individual subfamilies.
• GO (Gene Ontology) annotations and evidence codes.
• Other annotations and experimental data.
• Hyperlinks to papers and online resources.
• An analysis of the family's multiple sequence alignment using the subfamily decomposition to predict specificity positions defining the individual subtypes.
• A predicted structure, including construction of comparative models for some families.
• A predicted cellular localization (i.e., membrane-localized, secreted, cytoplasmic, nuclear, etc.)