A method for simultaneous alignment of multiple protein structures

  title={A method for simultaneous alignment of multiple protein structures},
  author={Maxim Shatsky and Ruth Nussinov and Haim J. Wolfson},
  journal={Proteins: Structure},
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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MultiProt - A Multiple Protein Structural Alignment Algorithm
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.
MUSTA - A General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins
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.
MASS: multiple structural alignment by secondary structures
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.
Multiple structural alignment by secondary structures: Algorithm and applications
By using conserved structural motifs, one can guide protein–protein docking, which is a notoriously difficult problem and is shown to be a combination of several important characteristics of MASS.
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A novel technique for the alignment of flexible proteins that does not require an a priori knowledge of the flexible hinge regions and allows un‐predefined hinge‐based motions.
Automated multiple structure alignment and detection of a common substructural motif
A multiple structural alignment algorithm that automatically finds the largest common substructure (core) of Cα atoms that appears in all the molecules in the ensemble and can be applied to protein surfaces, protein–protein interfaces and protein cores to find the optimally, and suboptimally spatially recurring substructural motifs.
Protein structure comparison by alignment of distance matrices.
A novel algorithm (DALI) for optimal pairwise alignment of protein structures that identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions is developed.
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The algorithm encoded in STAMP (Structural Alignment of Multiple Proteins) is shown to give alignments in good agreement with published structural accounts within the dehydrogenase fold domains, globins, and serine proteinases.
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A new algorithm is reported which builds an alignment between two protein structures. The algorithm involves a combinatorial extension (CE) of an alignment path defined by aligned fragment pairs
Protein Threading Based on Multiple Protein Structure Alignment.
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    Genome informatics. Workshop on Genome Informatics
  • 1999
A simple dynamic-programming based algorithm which uses a profile matrix obtained from the result of multiple structure alignment to compute a threading, and participated in the threading category of CASP3 (Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction).