Scoring and Ranking of Sequence-Structure Alignments. Quasar is used to score and rank sequence and structure alignments.

With the growing gap between the number of known protein sequences in databases like SwissProt/TrEMBL and the number of experimentally determined protein structures in the PDB, automated structure prediction methods like homology modeling and fold recognition have become valuable tools for assigning potential folds to new protein sequences.

A wide range of structure prediction servers is available on the web that offer a variety of possibilities for generating structural alignments of a query protein to a template protein with known 3D structure. Nevertheless, identifying the "best" structural alignment in a set of sequence-structure alignments (possibly coming from different sources) remains a difficult task.

The Quasar system was designed to make it possible to explore, benchmark, optimize and use various methods to rank comparative modelling and fold recognition alignments (also called sequence-structure alignments) easily with respect to a user defined scoring formula.

In order to support the process of finding and using such a formula, Quasar offers the possibility to combine one or more scoring schemes in a linear or non-linear formula with help of a score conductor that can be used afterwards to calculate a quality score for all alignments in an alignment file.
Quasar already provides a number of common alignment quality measurements (= scoring schemes) like different amino acid exchange matrices (PAM, Blosum, conformational matrices...) and secondary structure measures like SOV or Q3.

Scoring schemes can easily be combined in a scoring formula that is represented by a score conductor, e.g. a weighted sum, in the Quasar environment. Additionally Quasar provides the possibility to add new scoring schemes or score conductors to the system as well as to the graphical user interface (GUI) such that Quasar can easily be extended to fit your needs.

Requirements:
* Java

The license of this software is Freeware, you can free download and free use this cad software.