PROFESS: a PROtein Function, Evolution, Structure and Sequence database

Abstract

The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are ∼1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein–protein interaction networks.Database URL: http://cse.unl.edu/∼profess/

Bacterial protein structures reveal phylum dependent divergence

“…Additionally, each protein was annotated with GO numbers and the relative functional similarity for each COG was measured (Table 1). This was achieved by developing the PROFESS database (Triplet, et al, 2010) that contains the PDB to COG annotations among other biologically relevant information. This includes associating each structure with its phyla classification, which allowed for the structures from Firmicutes and Proteobacteria to be easily selected for further analysis (Table S1).…”

“…A single PDB file may contain multiple protein chains, where each chain may have a separate COG assignment. All structure information is stored in our PROFESS ( PRO tein F unction, E volution S equence and S tructure) database (Triplet, et al, 2010), which is parsed to find the largest Z-score for each pairwise structure comparison. The largest Z-score represents the best structure comparison for a pair of proteins and ensures that the correct PDB chains were used for the analysis and the correct COG assignments were made.…”

Searching the protein structure database for ligand-binding site similarities using CPASS v.2

“…Specifically, the results table now contains a column that contains a description of the function associated with each matched ligand-defined binding site. An additional column was also added that lists the eggNOG ( http://eggnog.embl.de/ ) functional classification identification number [ 32 ], providing a direct link to a summary page in our PROtein Function, Evolution, Structure and Sequence (PROFESS) database ( http://cse.unl.edu/~profess/ ) [ 33 ]. In this manner, it is now trivial to ascertain if a prevalent functional classification is apparent from a CPASS analysis.…”

Cubic Spline Interpolation Reveals Different Evolutionary Trends of Various Species

“…In the past, evolutionary biologists could make only relatively subjective statements about the speed of evolution. However, the DNA data available today in many genome databases [5], [13] for an increasing number of living species and even from ancient DNA from fossils enables modern evolutionary biologists to make more precise and measurable statements about the speed of evolution. This is because the speed of biological evolution from an ancestor species to a descendant species can be measured in the number of genetic mutations.…”