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Improving your target-template alignment with MODalign

Barbato, Alessandro ; Benkert, Pascal ; Schwede, Torsten ; Tramontano, Anna ; Kosinski, Jan

In: Bioinformatics, 2012, vol. 28, no. 7, p. 1038-1039

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    Title
    • Improving your target-template alignment with MODalign
    Author
    • Barbato, Alessandro. Department of Physics, Sapienza University P.le A. Moro, 5, 00185 Rome, Italy, Biozentrum, University of Basel, SIB Swiss Institute of Bioinformatics, Basel, Switzerland and Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Sapienza University, P.le A. Moro 5, 00185 Rome, Italy
    • Benkert, Pascal. Department of Physics, Sapienza University P.le A. Moro, 5, 00185 Rome, Italy, Biozentrum, University of Basel, SIB Swiss Institute of Bioinformatics, Basel, Switzerland and Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Sapienza University, P.le A. Moro 5, 00185 Rome, Italy
    • Schwede, Torsten. Department of Physics, Sapienza University P.le A. Moro, 5, 00185 Rome, Italy, Biozentrum, University of Basel, SIB Swiss Institute of Bioinformatics, Basel, Switzerland and Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Sapienza University, P.le A. Moro 5, 00185 Rome, Italy
    • Tramontano, Anna. Department of Physics, Sapienza University P.le A. Moro, 5, 00185 Rome, Italy, Biozentrum, University of Basel, SIB Swiss Institute of Bioinformatics, Basel, Switzerland and Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Sapienza University, P.le A. Moro 5, 00185 Rome, Italy
    • Kosinski, Jan. Department of Physics, Sapienza University P.le A. Moro, 5, 00185 Rome, Italy, Biozentrum, University of Basel, SIB Swiss Institute of Bioinformatics, Basel, Switzerland and Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Sapienza University, P.le A. Moro 5, 00185 Rome, Italy
    Document Type
    • Postprint
    OAI-PMH Identifier
    • oai:doc.rero.ch:289322
    Summary
    Summary: 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. Availability and implementation: Freely available on the web at http://modorama.biocomputing.it/modalign. Website implemented in HTML and JavaScript with all major browsers supported. Contact: jan.kosinski@uniroma1.it