:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
UniAlign: Protein Structure Alignment Meets Evolution.
Zhao C, Sacan A.
Bioinformatics. 2015 Jun 9. pii: btv354.
:: DESCRIPTION
mulPBA is an efficient tool for comparison of protein structures based on similarity in the local backbone conformation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
SALAMI (STRUCTURE ALIGNMENT AND MATCH INQUIRY) takes a protein structure (PDB format) or asks for the name of a PDB file. This is then compared against structures from the PDB. After about 20 minutes, you will receive a set of structural alignments, completely independent of sequence identity. The service is similar to that provided by dali.
::DEVELOPER
Center for Bioinformatics (ZBH), University of Hamburg
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W480-4. doi: 10.1093/nar/gkp431. Epub 2009 May 22.
The SALAMI protein structure search server.
Margraf T1, Schenk G, Torda AE.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: DESCRIPTION
FATCAT server is a pairwise flexible protein structure alignment server.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
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.
:: DESCRIPTION
POSA server is a multiple flexible protein structure alignment server using a partial order graph representation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
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.