:: DESCRIPTION
modplus is a wrapper script for Modeller; it performs sequence-structure alignment and preprocessing steps to model target sequence. The input to the program is a multiple alignment of target and template sequences in the FASTA format. The template structures will be supposed to be accessible in a given location.
::DEVELOPER
Laboratory of Bioinformatics, VU Institute of Biotechnology
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SAP is a software of pairwise protein structure alignment via double dynamic programming.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Taylor W.R.,
Protein structure comparison using SAP.
Methods Mol. Biol. 143 (2000) 19-32.
:: DESCRIPTION
PROMALS3D (PROfile Multiple Alignment with predicted Local Structures and 3D constraints) constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PROMALS3D: a tool for multiple sequence and structure alignment.
Jimin Pei, Bong-Hyun Kim and Nick V. Grishin.
Nucleic Acids Res. 2008 36(7):2295-2300.
:: DESCRIPTION
SAMO is a protein Structure Alignment tool based on Multiple Objective optimization.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Luonan Chen, Ling-Yun Wu, Yong Wang, Shi-Hua Zhang and Xiang-Sun Zhang.
Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.
BMC Structural Biology, Vol. 6, 18, 2006.
:: DESCRIPTION
SANA is an algorithm for the alignment of two proteins. Specifically, core regions in two protein structures are first aligned by identifying connected components in a network of neighboring, geometrically compatible aligned fragment pairs (AFPs). The initial alignments then are refined through a multi-objective optimization method. The algorithm can produce both sequential and non-sequential alignments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lin Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen.
SANA: an algorithm for sequential and non-sequential protein structure alignment.
Amino Acids. 2010 Jul;39(2):417-25. Epub 2010 Feb 2.
:: DESCRIPTION
SABIC is a software for protein structure alignment based on the internal coordinates (i.e. bond lengths, bond angles and torsion angles) of structure representation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Shen YF, Li B, and Liu ZP
Protein Structure Alignment Based on Internal Coordinates.
Interdisciplinary Sciences: Computational Life Sciences, 2:308-319, 2010.
:: DESCRIPTION
Compare3D is used to analyze the structure alignment of two or more polypeptide chains. The alignment is provided by the user, and is thus designed as a visual front end to another program.Compare3D applet uses temporary POM (Property Object Model) database generated in user specified scratch directory. This database contain 3D structure and alignment information provided by user as files in PDB format and alignment information.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Shindyalov IN, Bourne PE.
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm.
Nucleic Acids Res. 2001 Jan 1;29(1):228-9.
