Inference of Protein Function from Protein Structure

Inference of protein function from protein structure.

Structural genomics has brought us three-dimensional structures of proteins with unknown functions. To shed light on such structures, we have developed ProKnow (http://www.doe-mbi.ucla.edu/Services/ProKnow/), which annotates proteins with Gene Ontology functional terms. The method extracts features from the protein such as 3D fold, sequence, motif, and functional linkages and relates them to fu...

Global mapping of the protein structure space and application in structure-based inference of protein function.

We have constructed a map of the "protein structure space" by using the pairwise structural similarity scores calculated for all nonredundant protein structures determined experimentally. As expected, proteins with similar structures clustered together in the map and the overall distribution of structural classes of this map followed closely that of the map of the "protein fold space" we have r...

Structure-based function inference using protein family-specific fingerprints.

We describe a method to assign a protein structure to a functional family using family-specific fingerprints. Fingerprints represent amino acid packing patterns that occur in most members of a family but are rare in the background, a nonredundant subset of PDB; their information is additional to sequence alignments, sequence patterns, structural superposition, and active-site templates. Fingerp...

Structure-Based Protein Functional Inference

Proteins sharing similar molecular functions are found to co-localize in MAP2000, pointing towards a new scheme for structure-based functional inference for remote homologues using calculated distances between proteins in the map. Here, we present a method that uses the distances in the MAP2000 fold space to predict functionally similar protein pairs. We found that this scheme consistently outp...

Protein structure and function from sequences