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. 2012 Apr 1;28(7):1038-9.
doi: 10.1093/bioinformatics/bts070. Epub 2012 Feb 4.

Improving your target-template alignment with MODalign

Alessandro Barbato  1 , Pascal Benkert, Torsten Schwede, Anna Tramontano, Jan Kosinski
Affiliations

Improving your target-template alignment with MODalign

Alessandro Barbato et al. Bioinformatics. .

Abstract

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.

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Figures

Fig. 1.
Fig. 1.
The MODalign result page. The alignment can be edited in the target-template alignment section. When the alignment is modified, the output, such as coloring by sequence conservation or highlighting of potential errors, is modified in real time, while QMEAN can be recalculated on request.
See this image and copyright information in PMC

References

    1. Benkert P., et al. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics. 2011;27:343–350. - PMC - PubMed
    1. Cheng J., et al. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res. 2005;33:W72–W76. - PMC - PubMed
    1. Fraternali F., Cavallo L. Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome. Nucleic Acids Res. 2002;30:2950–2960. - PMC - PubMed
    1. Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 1999;292:195–202. - PubMed
    1. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983;22:2577–2637. - PubMed

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