alignments in YASARA
In addition to a classical superposition that
minimizes the RMSD between two atom selections, YASARA supports a
number of special features:
- Chemically equivalent
atoms can be flipped automatically to minimize the RMSD. For
example when calculating the heavy-atom RMSD between two proteins, it
may happen that a certain Phe side-chain has been flipped by 180
degrees, i.e. the CD1/CE1 atoms have swapped place with CD2/CE2.
Chemically the result is identical, yet a wrong RMSD will be calculated
if the atoms are not flipped back. YASARA supports this flipping for
all kinds of molecules by analyzing the structure to search for
equivalent atoms to flip.
- Simultaneous superposition
of multiple objects on their core regions. When
calculating an NMR structure, it is usually needed to superpose the
resulting bundle of structures all together, putting most
emphasis on the core regions, so that the superposition is not
negatively influenced by floppy tails. To achieve this goal, YASARA
features the THESEUS maximum likelihood method.
- Structural alignments.
If it is not known which atoms should actually be superposed, one needs
to create an alignment first. When working with proteins, the most
successful approach is to ignore the sequence and concentrate on the
structure only. This allows to superpose also distantly related
proteins with high accuracy. A large number structural alignment
have been developed. YASARA has a built-in MUSTANG module and a local
plugin for SHEBA in Linux and MacOS.
- Twisted structural alignments. YASARA can bend and wind proteins to maximize the number of structurally aligned residues, for example to create sequence profiles for homology modeling.
- Structural alignments of small molecules.
YASARA Model and above can automatically locate the largest common
substructure of small molecules like ligands and superpose them.
- Multiple structural
alignments. If the goal is to align and superpose an entire
protein family, the required multiple structural alignment can be
performed with the built-in MUSTANG module.
- Identify related structures in the PDB.
An interface to the RCSB's weekly updated all-against-all comparison of
PDB entries makes it trivial to retrieve and align all structurally
related proteins to a given input structure.
- Sequence alignments.
In some rare applications, one needs to superpose proteins based on a
sequence alignment. YASARA supports local Smith&Waterman and
global Needleman&Wunsch sequence alignments to achieve this goal.
R E F E R E N C E S
 THESEUS: maximum likelihood superpositioning and analysis of
Theobald DL, Wuttke DS (2006) Bioinformatics 22 ,2171-2172
 MUSTANG: A multiple structural alignment algorithm
Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM (2006) Proteins 64,559-574
 J.Jung & B.Lee, (2000) Protein Eng. 13,535-543
 I.N.Shindyalov & P.E.Bourne (1998) Protein Eng. 11,739-747
 M.Shatsky,R.Nussinov & H.J.Wolfson (2002) Lect.Notes in