Tag: Structural Alignment

ProtDeform 1.0 – Protein Structural Alignment

ProtDeform 1.0

:: DESCRIPTION

ProtDeform is a protein structural alignment. It automatically finds the alignments that expert hands define as most likely, and to recognize domains with the same CATH homology and topology.

::DEVELOPER

Computational Biology and Bioinformatics Research Group , University of the Balearic Islands

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 ProtDeform

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jul 1;25(13):1625-31. doi: 10.1093/bioinformatics/btp296.
Flexible structural protein alignment by a sequence of local transformations.
Rocha J, Segura J, Wilson RC, Dasgupta S.

MISTRAL – Multiple Protein Structural Alignment

MISTRAL

:: DESCRIPTION

MISTRAL is  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.

::DEVELOPER

The Institut de Physique Théorique (IPhT)

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Oct 15;25(20):2663-9. doi: 10.1093/bioinformatics/btp506. Epub 2009 Aug 19.
MISTRAL: a tool for energy-based multiple structural alignment of proteins.
Micheletti C1, Orland H.

VISTAL – Two-dimensional Visualization tool for Structural Alignments

VISTAL

:: DESCRIPTION

VISTAL (VISualizing Structural Alignments) describes structures as a series of secondary structure elements, and places matched residues one on top of each other colored according to the three-dimensional distance of their Ca atoms.

::DEVELOPER

Rachel Kolodny

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  VISTAL

:: MORE INFORMATION

Citation

Kolodny, R. and Honig, B. (2006)
VISTAL – A New 2D Visualization Tool of Protein 3D Structural Alignments.
Bioinformatics 22:2166-2167.

MAMMOTH 1.2 / MAMMOTH-mult – Protein Structural Alignment

MAMMOTH 1.2 / MAMMOTH-mult

:: DESCRIPTION

MAMMOTH (Matching Molecular Models Obtained from Theory) is a sequence-independent protein structural alignment method.

MAMMOTH-mult is a multiple alignment version of MAMOTH. It multiply aligns protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned.

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MAMMOTH , MAMMOTH-mult

:: MORE INFORMATION

Citation

A new progressive-iterative algorithm for multiple structure alignment.
Lupyan D, Leo-Macias A, Ortiz AR.
Bioinformatics. 2005 Aug 1;21(15):3255-63. Epub 2005 Jun 7.

MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison.
Ortiz AR, Strauss CE, Olmea O.
Protein Sci. 2002 Nov;11(11):2606-21.

CONSAN 1.2 – Pairwise Structural RNA Alignment

CONSAN 1.2

:: DESCRIPTION

CONSAN is a software of pairwise RNA structural alignment, both unconstrained and constrained on alignment pins.

::DEVELOPER

Robin Dowell, Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CONSAN

:: MORE INFORMATION

Citation

Dowell, RD and Eddy, SR.
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.
BMC Bioinformatics 2006, 7:400 .

LIGSIFT – Ligand Structural Alignment and Virtual Screening

LIGSIFT

:: DESCRIPTION

LIGSIFT is a new computational method for the structural alignment of small molecules.

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LIGSIFT

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 21. pii: btu692.
LIGSIFT: An open-source tool for ligand structural alignment and virtual screening.
Roy A, Skolnick J

iAlign 1.1 – Structural alignment for protein-protein

iAlign 1.1

:: DESCRIPTION

iAlign is a program designed for the comparison of the structures of protein-protein interfaces.

Proteins usually do not act alone. From macromolecular machinery to antibody/antigen complexes, protein-protein interactions play an essential role in a living cell. How do proteins interact with each other? High resolution structures of protein-protein complexes provide valuable insights into the mechanisms of protein-protein interactions. Structural comparison of protein-protein interfaces further facilitates studies of protein-protein interaction modes and helps to infer relationship between proteins

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 iAlign

:: MORE INFORMATION

Citation

M. Gao and J. Skolnick, 2010.
iAlign: a method for the structural comparison of protein-protein interfaces.
Bioinformatics, 26(18):2259-65.

PredUs 1.2.0 – Prediction of Protein Interfaces Using Structural Alignment

PredUs 1.2.0

:: DESCRIPTION

PredUs is a flexible, interactive, template-based webserver to predict protein-protein interface of a given monomeric query protein using its close and remote structural neighbors.

::DEVELOPER

Barry Honig’s group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PredUs: a web server for predicting protein interfaces using structural neighbors.
Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W283-7. doi: 10.1093/nar/gkr311.

TM-align 20150914 – Quick & Accurate Structural Alignment

TM-align 20150914

:: DESCRIPTION

TM-align is a computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrix.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 TM-align

:: MORE INFORMATION

Citation

Y. Zhang, J. Skolnick,
TM-align: A protein structure alignment algorithm based on TM-score ,
Nucleic Acids Research, 2005 33: 2302-2309

MM-align 20130815 – Protein Complex Structural Alignment

MM-align 20130815

:: DESCRIPTION

MM-align is an algorithm for structurally aligning multiple-chain protein-protein complexes. The algorithm is built on a heuristic iteration of a modified Needleman-Wunsch dynamic programming (DP) algorithm, with the alignment score specified by the inter-complex residue distances. The multiple chains in each complex are first joined, in every possible order, and then simultaneously aligned with cross-chain alignments prevented. The alignments of interface residues are enhanced by an interface-specific weighting factor.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 MM-align

:: MORE INFORMATION

Citation

S. Mukherjee, Y. Zhang,
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.
Nucleic Acids Research 2009; 37: e83

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