Improving your target-template alignment with MODalign.
CONCLUSIONS
MODalign is an interactive web-based tool aimed at helping protein structure modelers to inspect and manually modify the alignment between the sequences of a target protein and of its template(s). It interactively computes, displays and, upon modification of the target-template alignment, updates the multiple sequence alignments of the two protein families, their conservation score, secondary structure and solvent accessibility values, and local quality scores of the implied three-dimensional model(s). Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information.


METHODS
Freely available on the web at http://modorama.biocomputing.it/modalign. Website implemented in HTML and JavaScript with all major browsers supported.


BACKGROUND
jan.kosinski@uniroma1.it.
Department of Physics, Sapienza University P.le A. Moro, 5, 00185 Rome, Italy.
Alessandro
A
Barbato
Pascal
P
Benkert
Torsten
T
Schwede
Anna
A
Tramontano
Jan
J
Kosinski
D020407:Internet; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D011506:Proteins