FATCAT – Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists

FATCAT

:: DESCRIPTION

FATCAT server is a pairwise flexible protein structure alignment server.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2003 Oct;19 Suppl 2:ii246-55.
Flexible structure alignment by chaining aligned fragment pairs allowing twists.
Ye Y, Godzik A.

POSA – Partial Order Structure Alignment

POSA

:: DESCRIPTION

POSA server is a multiple flexible protein structure alignment server using a partial order graph representation.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

POSA: a user-driven, interactive multiple protein structure alignment server.
Li Z, Natarajan P, Ye Y, Hrabe T, Godzik A.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W240-5. doi: 10.1093/nar/gku394.

SALIGN r180 – Multiple Protein Sequence/Structure Alignment Server

SALIGN r180

:: DESCRIPTION

SALIGN is a general alignment module of the modeling program MODELLER. The alignments are computed using dynamic programming, making use of several features of the protein sequences and structures

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 1;28(15):2072-3. doi: 10.1093/bioinformatics/bts302. Epub 2012 May 21.
SALIGN: a web server for alignment of multiple protein sequences and structures.
Braberg H1, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS.

jCE/jFATCAT 20150427 – Calculate Structure Alignment

jCE/jFATCAT 20150427

:: DESCRIPTION

CE (Combinatorial Extension) is a method for calculating pairwise structure alignments. CE aligns two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. Matches are termed aligned fragment pairs (AFPs). Heuristics are used in defining a set of optimal paths joining AFPs with gaps as needed. The path with the best RMSD is subject to dynamic programming to achieve an optimal alignment. For specific families of proteins additional characteristics are used to weight the alignment.

jCE is a re-implementation of the original CE source code in the Java programming language. While the algorithm is principle exactly the same as in the original implementation

jFatCat is a re-implementation of the FATCAT algorithm in the Java programming language.

::DEVELOPER

Andreas Prlić(andreas@sdsc.edu) , Philip E. Bourne(bourne@sdsc.edu)

:: SCREENSHOTS

jCE

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 jCE/jFATCAT

:: MORE INFORMATION

Citation

Shindyalov IN, Bourne PE (1998)
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
Protein Engineering 11(9) 739-747.

Precalculated Protein Structure Alignments at the RCSB PDB website
Andreas Prlic; Spencer Bliven; Peter W Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq572

SAS-Pro 201106 – Sequential and Non-sequential Structure Alignment of Proteins

SAS-Pro 201106

:: DESCRIPTION

The SAS-Pro software provides an optimal structural alignment between any given pair of proteins. It is based on an algorithm for Simultaneous Alignment and structure Superposition of PROteins (SAS-Pro). SAS-Pro provides both sequential and non-sequential protein alignments.

::DEVELOPER

Nikolaos V. Sahinidis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MATLAB
  • gfortran compiler 4.4.1 or newer version

:: DOWNLOAD

 SAS-Pro

:: MORE INFORMATION

Citation

S. B. Shah and N. V. Sahinidis,
SAS-Pro: Simultaneous Residue Assignment and Structure Superposition for Protein Structure Alignment,
PLoS ONE 7(5): e37493.

SPalign / SPalign-NS – Protein Structure Alignment

SPalign / SPalign-NS

:: DESCRIPTION

SPalign is a program that optimizes SP-score for structure alignment. SPalign was applied to recognize proteins within the same structure fold and having the same function of DNA or RNA binding.

SPalign-NS: Non-sequential Protein Structure Alignment

::DEVELOPER

Laboratory of Structural Bioinformatics and Design

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPalign , SPalign-NS

:: MORE INFORMATION

Citation

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.
Brown P, Pullan W, Yang Y, Zhou Y.
Bioinformatics. 2015 Oct 10. pii: btv580.

Proteins. 2012 Aug;80(8):2080-8. doi: 10.1002/prot.24100. Epub 2012 May 25.
A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction.
Yang Y1, Zhan J, Zhao H, Zhou Y.

MulPBA – Multiple Protein Structure Alignment

MulPBA

:: DESCRIPTION

mulPBA is an efficient tool for comparison of protein structures based on similarity in the local backbone conformation.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.
Léonard S, Joseph AP, Srinivasan N, Gelly JC, de Brevern AG.
J Biomol Struct Dyn. 2014 Apr;32(4):661-8. doi: 10.1080/07391102.2013.787026.

UniAlign – Protein Pairwise Structure Alignment with Evolution and Sequence Information

UniAlign

:: DESCRIPTION

UniAlign is a new protein pairwise structure alignment algorithm that incorporates additional evolutionary information captured in the form of sequence similarity, sequence profiles, and residue conservation.

::DEVELOPER

Sacan Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

 

:: MORE INFORMATION

Citation

UniAlign: Protein Structure Alignment Meets Evolution.
Zhao C, Sacan A.
Bioinformatics. 2015 Jun 9. pii: btv354.

GS-align – Glycan Structure Alignment and Similarity Measurement

GS-align

:: DESCRIPTION

GS-align is a novel computational method for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition, and the optimal alignment is determined by the maximum structural similarity score, GS-score whose significance is size-independent.

::DEVELOPER

Wonpil Im Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GS-align

:: MORE INFORMATION

Citation

GS-align for Glycan Structure Alignment and Similarity Measurement.
Lee HS, Jo S, Mukherjee S, Park SJ, Skolnick J, Lee J, Im W.
Bioinformatics. 2015 Apr 8. pii: btv202

STOVCA 3.95 – Comparison, Ranking and Evaluation of Structure Alignments

STOVCA 3.95

:: DESCRIPTION

STOVCA (STructural OVerlap CAlculator) is a software that takes as input a pairwise structure superposition of proteins, DNA or RNA in PDB format generated by any software and produces a standardized structural alignment and its corresponding similarity measures, according to the parameters provided by the user. Therefore, STOVCA allows the direct comparison and ranking of structural superpositions generated by any structure superposition software

::DEVELOPER

Francisco Melo Ledermann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX

:: DOWNLOAD

 STOVCA

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):47-53. doi: 10.1093/bioinformatics/bts600. Epub 2012 Oct 11.
Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments.
Slater AW1, Castellanos JI, Sippl MJ, Melo F.