ProHit

ProHit is our research tool for protein annotation. It supports bioinformatics researchers to find out as much as possible about their query sequences, their structures, their functions, and their relationships to other proteins.

Three fundamental search strategies

The power of bioinformatics rests on the redundancy and similarities among biological molecules. There are three fundamental search strategies which exploit these similarities:

	Sequence to sequence search: A sequence library is scanned to identify proteins or protein domains that have sequence similarities to the query sequence.
	Sequence to structure search: A library of 3D folds is scanned to identify proteins or protein domains that have a structure compatible with the query sequence.
	Structure to structure search: A library of 3D folds is scanned to identify proteins or protein domains that have similar structures to the query structure.

Integration of search tools

ProHit integrates these three fundamental search strategies into a single software tool by combining three powerful search tools PSI-Blast (sequence-sequence search), ProFit (sequence-structure search or fold recognition), and ProSup (structure-structure search).

Major challenges

The result of each search tool is a scored and sorted list of hits. The correct interpretation of these hit lists and the distinction of true positive from false positive hits is one of bioinformatics' major challenges.

Interpretation support through classification of proteins

ProHit's Hit Viewer is designed to support bioinformatics experts to efficiently and reliably identify true positive hits. This is achieved by ProWorld, ProCeryon's domain-based classification of proteins.

For more information please contact our Product Manager.

ProWorld

ProWorld is ProCeryon's expert-curated classification of protein domains annotated by fold, sequence, and function families. ProWorld contains all structures of the Brookhaven Protein Data Bank (PDB). ProWorld is updated regularly and open to include proprietary structures and data. When integrated into ProHit, ProWorld is a powerful tool for the fast and reliable identification of true positive hits.

ProSa-II

ProSa-II is a software package for analyis of the three-dimensional structure of proteins. The program generates scores reflecting the quality of structures. 'Bad' scores often correlate with incorrect structures or erroneous sections of a structure. The program also provides graphs of energy distributions which pinpoint problematic sections in the structure of a molecule.In protein engineering and design, ProSa-II is used to study the effect of mutations on the stability of a fold before the protein is expressed in vitro.

For more information please contact our Product Manager.