Multiple structure alignment software tools | Protein data analysis
Multiple protein structure alignment (MPStrA) is an important approach for functional and evolutionary analysis of groups of protein structures. Typically, MPStrA is used to identify the conserved regions that form the common structural core of a protein family.
Renders sequence similarities and secondary structure information for analysis and publication purposes. ESPript can assist users to optimize an alignment thank to its capability to display on the same figure the secondary structure information of each aligned sequence. It allows users to obtain an output from different files of aligned sequences. This tool is able to return the temperature factors replaced by similarity scores that it calculates.
A software tool used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.
Allows alignment of multiple sequences. MAFFT provides a range of different methods such as L-INS-I or FFT-NS-2. It permits to add unaligned sequences into an existing alignment. This tool can proceed to adjustment of direction in nucleotide alignment, constrained alignment and parallel processing. It employs the iterative refinement technique for calculation of progressive alignment.
Allows comparison of protein structures in 3D. DALI is a web server performing three types of structure comparisons: (1) Protein Data Bank (PDB) search, (2) pairwise comparison and (3) all against all structure comparison. The software is based on distance matrix comparison. It provides tools to navigate, integrate and organize some data pushed out by genomics and structural genomics.
Aims to fill the gap between the fast and widely used homology search programs, such as BLAST, PSI-BLAST, or HMMer/Pfam, and the very sensitive and accurate but rather inflexible and slow automated protein structure prediction servers. HHpred is therefore mainly meant to be used as an interactive function and structure prediction server, allowing, for example, to search various databases, to select templates manually, or to correct errors in the proposed target-template alignment. HHPred is part of the HH-suite and is available online or can be downloaded for local use.
Allows to compare protein structures in 3D. PDBeFold is the European Bioinformatics Institute-Macromolecular Structure Database (EBI-MSD) web service Secondary Structure Matching (SSM). The software, based on identification of residues occupying “equivalent” geometrical positions, provides multiple and multiple comparison, C-α alignment and examination similarity with the Protein Data Bank (PDB) archive or SCOP. User can also download and visualization best-superposed structures using various graphical packages.
Provides an alignment method that employs the Wu-Manber string-matching algorithm. Kalign was developed to calculate sequence distances and by incorporating local matches into the otherwise global alignment. It also supports nucleotide alignment, and an extension allows for external sequence annotation to be included into the alignment procedure. This method can be useful for large-scale comparative genomics.