Structure Based Sequence Alignment

Structure based sequence alignments are potentially more accurate than simple sequence alignments.The following programs and web utilities can help you in aligning, analyzing and annotating structural features (secondary structure elements, residues accessibility, hydropathy etc.) in integrated sequence and structure multiple alignments.

Integrated Sequence-Structure Analysis Platforms
open in new windowCn3D
Cn3D is an open-source code visualization tool for biomolecular structures, sequences, and sequence alignments. Cn3D is typically run from a web browser as a helper application for NCBI's Entrez system. Cn3D is the primary visualization tool for VAST alignments.
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Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA.
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open in new windowSTRAP
STRAP is a work bench for multiple sequence alignments of proteins. It is used to visualize three-dimensional structures, and to align several proteins using the sequences or the structure.
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Structure Based Sequence Alignment
open in new windowENDscript
A web server for searching homologous sequences and giving information on secondary structure elements, accessibility, hydropathy and protein-protein contacts.
open in new windowEXPRESSO (3DCoffee) This web server computes structure based multiple sequence alignments. You only need to provide the sequences. The server will automatically fetch the related structures and use them to guide the alignment.
open in new windowMICAlign MICAlign server takes inputs from a sequence and a template structure. The alignment algorithm incorporates multiple sources of information into a conditional random field model. The output of MICAlign is the sequence-to-structure alignment.
open in new windowPROMALS3D This web server 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.
Annotation Tools
open in new windowAline Interactive perl/tk application for editing and annotating multiple sequence alignments.  
open in new windowESPript
A web or standalone utility for structural annotation of multiple sequence alignments. ESPript is a utility to generate a pretty PostScript output from aligned sequences.
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open in new windowJOY JOY is a program to annotate protein sequence alignments with 3-D structural features.
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