POSA: a user-driven, interactive multiple protein structure alignment server

@article{Li2014POSAAU,
  title={POSA: a user-driven, interactive multiple protein structure alignment server},
  author={Jim Zhanwen Li and Padmaja Natarajan and Yuzhen Ye and Thomas Hrabe and Adam Godzik},
  journal={Nucleic Acids Research},
  year={2014},
  volume={42},
  pages={W240 - W245}
}
POSA (Partial Order Structure Alignment), available at http://posa.godziklab.org, is a server for multiple protein structure alignment introduced in 2005 (Ye,Y. and Godzik,A. (2005) Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21, 2362–2369). It is free and open to all users, and there is no login requirement, albeit there is an option to register and store results in individual, password-protected directories. In the updated POSA server described here, we… 

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References

SHOWING 1-10 OF 24 REFERENCES
SALIGN: a web server for alignment of multiple protein sequences and structures
TLDR
A web interface to SALIGN, the versatile protein multiple sequence/structure alignment module of MODELLER, which automatically determines the best alignment procedure based on the inputs, while allowing the user to override default parameter values.
Multiple flexible structure alignment using partial order graphs
TLDR
A new method of multiple protein structure alignment, POSA (Partial Order Structure Alignment), was developed using a partial order graph representation of multiple alignments and provides new insights by visualizing the mosaic nature of multiple structural alignments.
mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet
TLDR
A new web server is proposed called multiple Protein Block Alignment (mulPBA), which implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles, enabling the use of powerful sequence alignment methods for primary structure comparison.
CE-MC: a multiple protein structure alignment server
TLDR
The CE-MC server can be used to get multiple alignments for up to 25 protein structural chains with the flexibility of uploading multiple coordinate files and performing multiple structure alignment for user-selected PDB chains.
Smolign: A Spatial Motifs-Based Protein Multiple Structural Alignment Method
TLDR
This work introduces a novel strategy based on building a contact-window based motif library from the protein structural data, discovery and extension of common alignment seeds from this library, and optimal superimposition of multiple structures according to these alignment seeds by an enhanced partial order curve comparison method.
MUSTANG: A multiple structural alignment algorithm
TLDR
A reliable and robust algorithm, MUSTANG (MUltiple STructural AligNment AlGorithm), for the alignment of multiple protein structures, based on the progressive pairwise heuristic, which performs comparably to popular pairwise and multiple structural alignment tools for closely related proteins.
MUSTA - A General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins
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.
Matt: Local Flexibility Aids Protein Multiple Structure Alignment
TLDR
This work introduces the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations.
MISTRAL: a tool for energy-based multiple structural alignment of proteins
TLDR
MISTRAL (Multiple STRuctural ALignment), a novel strategy for multiple protein alignment based on the minimization of an energy function over the low-dimensional space of the relative rotations and translations of the molecules, is presented.
Multiple structure alignment with msTALI
TLDR
A program msTALI for aligning multiple protein structures that utilizes clear, informative features, allowing further customization for domain-specific applications, and is an effective algorithm for multiple structure alignment.
...
...