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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.

Source text:
(Li et al., 2014) POSA: a user-driven, interactive multiple protein structure alignment server. Nucleic Acids Res.

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MODELLER
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.
StatAlign
Samples from the joint posterior distribution of phylogenies, alignments and evolutionary parameters by applying the Markov chain Monte Carlo (MCMC) method. StatAlign also offers tools for efficient on-the-fly summarization of the results. This high-dimensional joint distribution can be analysed in several ways: the possibilities range from the simple statistics of marginalized single dimensions to the covariation analysis of multiple dimensions. StatAlign also provides the user with scores relating to the quality of a secondary structure prediction, such as information entropy values for the combined space of secondary structures and sampled alignments, and a reliability score that predicts the expected number of correctly predicted base-pairs.
Kpax
A fast protein structure alignment and database search program. Kpax uses Gaussian functions to score very rapidly the local and spatial environment of each amino acid residue in a protein, and it uses dynamic programming to find the optimal global alignment and superpositions of two proteins according to their Gaussian similarity scores. This approach allows very fast searches of structural databases, and it allows three-dimensional superpositions of proteins to be calculated rapidly. Kpax can perform flexible structure alignments, multiple structure alignments, and multiple flexible structure alignments. It can also score alignments calculated by other programs.
PSSweb / Protein Structural Statistics web server
A web server for protein structural statistics. PSSweb takes as input an ensemble of PDB files of protein structures, performs a multiple sequence alignment and computes structural statistics for each position of the alignment. Different optional functionalities are proposed: structure superposition, Cartesian coordinate statistics, dihedral angle calculation and statistics, and a cluster analysis based on dihedral angles. An interactive report is generated, containing a summary of the results, tables, figures and 3D visualization of superposed structures.
BAli-Phy
Estimates the alignment and phylogenetic tree that relate molecular sequences. BAli-Phy is a Bayesian program that includes a number of tools to summarize the joint posterior samples. It can also sample from traditional phylogenetic models in which the alignment of the leaf sequences is fixed. It finally implements several continuous-time Markov chain (CTMC) processes for residue-substitution, including nucleotide models, several codon-based models and empirically estimated amino acid models.
M-Coffee
Uses consistency to estimate a consensus alignment. M-Coffee is an extension of T-Coffee and a meta-method for assembling multiple sequence alignments (MSA) by combining the output of several individual methods into one single MSA. This method outperforms all the individual methods on three major reference datasets: HOMSTRAD, Prefab and Balibase. It is on average 1–3 point percent more accurate than the best individual method and nearly twice more likely to deliver the best multiple alignment.
MUMMALS / MUltiple alignment with Multiple MAtch state models of Local Structure
Improves alignment quality by using pairwise alignment hidden Markov models (HMMs) with multiple match states that describe local structural information without exploiting explicit structure predictions. MUMMALS is a progressive multiple sequence alignment program that achieves statistically best accuracy among several leading aligners, such as ProbCons, MAFFT and MUSCLE, albeit the average improvement is small, in the order of several percent.
3dSS / 3-Dimensional Structural Superposition
New
Enables the superposition of two or several 3D protein structures. 3dSS is a web server, built for the research community working in the area of structural bioinformatics, that superposes either complete or partial structures. The software deploys STAMP and ProFit for superposition purposes and interfaces the molecular visualization tool RASMOL to view the superposed molecules in the client machine. It can serve to identify the invariant and common water molecules.
SuperPose
New
Allows calculation of pairwise and multiple protein structure superpositions. SuperPose is a web server that performs a wide range of sophisticated structural superpositions. The software combines sequence alignment and difference distance matrix calculations to constrain its quaternion eigenvalue superposition calculations. It provides a wide range of interactive viewing options. SuperPose generates several textual and visual outputs allowing users to explore and compare complex protein structures.
STRAP / STRuctural Alignments of Proteins
A versatile workbench for protein analysis that can be used to generate and refine multiple alignments, to download PDB files from public ftp servers, visualize protein structural data with plugin or integrated protein structure viewers, and to map mutations onto three dimensional protein structures. Users can load multiple protein sequences or structures into the main STRAP user interface, and simultaneously develop plugins using an editor of their choice such as Emacs.
PyMod
Acts as simple and intuitive interface between PyMOL and several bioinformatics tools (i.e., PSI-BLAST, Clustal Omega, MUSCLE, CAMPO, PSIPRED, and MODELLER). PyMod builds homology models through the popular MODELLER package. Starting from the amino acid sequence of a target protein, users may take advantage of PyMod to carry out the three steps of the homology modeling process (that is, template searching, target-template sequence alignment and model building) in order to build a 3D atomic model of a target protein (or protein complex). Additionally, PyMod may be used outside the homology modeling context, in order to extend PyMOL with numerous types of functionalities. Sequence similarity searches, multiple sequence-structure alignments and evolutionary conservation analyses can all be performed in the PyMod 2.0/PyMOL environment.
PCMA / Profile Consistency Multiple sequence Alignment
Applies the fast algorithm of ClustalW to align highly similar sequences and the T-Coffee algorithm to align the relatively divergent pre-aligned groups. PCMA is a progressive multiple sequence alignment program that combines these two different alignment strategies. To properly balance speed and accuracy, PCMA takes into account both sequence diversity and the user’s preferences. The alignment speed is closely related to the average identity threshold, which the user can set.
Opal
A package for aligning multiple biological sequences. Opal attains accuracy on par with the state-of-the-art without altering the alignment scoring function by increasing gap penalties near hydrophobic regions, or through position specific substitution scores based on alignment consistency. With this heuristic, the alignment between two sequences in a group is not altered when new sequences are added to the group. Over all benchmarks, the median run time for Opal was less than 10 seconds, which was on an input of 20 sequences of length about 250.
3DCOMB
A package to generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise alignments. 3DCOMB is unique in that it makes use of both local and global structure environments, combined by a statistical learning method, to accurately identify highly similar fragment blocks (HSFBs) among all proteins to be aligned. 3DCOMB significantly excels others in aligning distantly related proteins. It can also generate correct alignments for functionally similar regions among proteins of very different structures while many other MSA tools fail. 3DCOMB is useful for many real-world applications..
Mustguseal
Assists in building large structure-guided sequence alignments of functionally diverse protein families. Mustguseal offers users possibility to download the final alignment for a local utilization. This final alignment can be operated on-line with the built-in interactive tools and further submitted to the integrated sister web-servers of Mustguseal. This operation permits users to analyze conserved, subfamily-specific, and co-evolving residues for studying a protein function and regulation.
IBiSS / Integrative Biology of Sequences and Structures
A web-based tool that is designed for interactively displaying 3D structures and selected sequences of subunits from large macromolecular complexes thus allowing simultaneous structure-sequence analysis such as conserved residues involved in catalysis or protein-protein interfaces. This tool comprises a Graphic User Interface and uses a rapid-access internal database, containing the relevant pre-aligned multiple sequences across all species available and 3D structural information. These annotations are automatically retrieved and updated from UniProt and crystallographic and cryo-EM data available in the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB).
SiteBinder
Allows for the multiple superimposition of large sets of protein structural motifs. SiteBinder performs a systematic search for the atom pairing that provides the best fit. During this search, the root-mean-square deviation (RMSD) values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using protein data bank (PDB) annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. SiteBinder is able to process up to thousands of protein structural motifs in a very short time, and provides an intuitive and user-friendly interface. This interface consists of three basic elements: the rendering view, the input panel, and the results panel. The input panel includes the list of motifs and the selection tree. SiteBinder is freely available online.
MUSTANG / MUltiple STructural AligNment AlGorithm
A package which reports the multiple sequence alignment and the corresponding superposition of structures. MUSTANG aligns residues on the basis of similarity in patterns of both residue-residue contacts and local structural topology. The tool also uses a progressive pairwise framework to build the final multiple structural alignment. In comparison with the performance of DALI at a pairwise level, and with other multiple structural alignment tools such as POSA, CE-MC, MALECON, and MultiProt, MUSTANG is very reliable in generating quality multiple structural alignments even on very distantly-related data sets containing structural deformations.
Superpose3D
Allows local structural comparison. Superpose3D allows users to flexibly specify the way that residues are to be represented during the computation and the pairing rules. The software also allows definition of the pseudo-atoms that represent each residue (including modified amino acids) by referring to the standard Protein Data Bank (PDB) atom naming convention. It can be useful for studying ligand binding sites, enzyme active sites or protein/protein interaction surfaces for instance.
SARpred
A neural network based method predicts the real value of surface accessibility (SA) by using multiple sequence alignment. In this method, two feed forward, back-propagation networks are used. The first sequence-to-structure network is trained with PSI-BLAST generated position specific scoring matrices. Further, the initial predictions from the first network and PSIPRED predicted secondary structure are used as input to the second structure-to-structure network. The input is a single letter-code amino acid sequence in free format and output is a real value of surface accessibility corresponding to the amino acid sequence.
StralSV / Structure Alignment-based Sequence Variability
Implements a structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. Input parameters to StralSV (window_size, distance_cutoff, or span_size) can be varied in order to adjust the stringency with which structure fragments are selected or with which local alignments are made, thereby providing the user with flexibility in detecting similar structure fragments. Furthermore, StralSV safeguards against degradation of sequence variability data quality by enforcing structure context upon local alignments in a two-step process of identifying "qualified" hits.
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