A method for simultaneous alignment of multiple protein structures

@article{Shatsky2004AMF,
  title={A method for simultaneous alignment of multiple protein structures},
  author={Maxim Shatsky and Ruth Nussinov and Haim J. Wolfson},
  journal={Proteins: Structure},
  year={2004},
  volume={56}
}
Here, we present MultiProt, a fully automated highly efficient technique to detect multiple structural alignments of protein structures. MultiProt finds the common geometrical cores between input molecules. To date, most methods for multiple alignment start from the pairwise alignment solutions. This may lead to a small overall alignment. In contrast, our method derives multiple alignments from simultaneous superpositions of input molecules. Further, our method does not require that all input… 
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References

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TLDR
A fully automated highly efficient technique which detects the multiple structural alignments of protein structures and presents new multiple structural alignment results of protein families from the All beta proteins class in the SCOP classification.
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TLDR
An algorithm designed to carry out multiple structure alignment and to detect recurring substructural motifs that is applicable to comparisons of RNA structures and to detection of a pharmacophore in a series of drug molecules is presented.
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An important novel feature of MASS is subset alignment detection: It does not require that all the input molecules be aligned, and is capable of detecting structural motifs shared only by a subset of the molecules.
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TLDR
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