YASARA Structure features a loop modeler, that
can quickly retrieve loop conformations that bridge two sets of anchor
residues from the Protein Data Bank. This knowledge-based approach
benefits enormously from the steadily growing PDB, and has been shown
to be a strong competition for ab-initio
- A non-redundant subset of the PDB (90% sequence
identity cutoff) forms the database from which the loop
conformations can be retrieved. Currently the database contains ~14000
complete protein chains.
- Since complete chains are stored in the
are not limited to loops. It is easily possible to extract e.g. all
fragments spanning two selected anchor points that contain 10 helical
residues in the middle.
- For loops up to 18 residues long, a database
to retrieve the hits within a fraction of a second. Longer loops take
around a minute to model.
- The loop conformations extracted from the
ranked by a combined quality score, that considers sequence similarity,
bumps with the rest of the structure, and the fit to the terminal loop
- Since loops extracted from a database do
normally not fit
the anchor points exactly, they are closed using cyclic coordinate
descent, an algorithm developed to steer robotic arms.
- To identify the best conformation of
of database hits, YASARA analyzes the loops sequentially, optimizing
side-chains of loop- and surrounding residues, and calculating
interaction and solvation energies, including knowledge based dihedral
and packing components.
R E F E R E N C E S
 Loops In Proteins (LIP) - a
comprehensive loop database for homology modelling
Michalsky E, Goede A and Preissner R (2003) Protein Engineering 16, 979-985
 PISCES: a
protein sequence culling server
Wang G and Dunbrack RL Jr. (2003) Bioinformatics 19, 1589-1591
coordinate descent: A robotics algorithm for protein loop closure
Canutescu AA and Dunbrack RL Jr. (2003)Protein Sci. 12, 963-972
graph-theory algorithm for
rapid protein side-chain prediction
Canutescu AA, Shelenkov AA and Dunbrack RL Jr. (2003), Protein Sci. 12,2001-2014.