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MAFFT

Obsolete
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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.

BAli-Phy

A Bayesian posterior sampler that employs Markov chain Monte Carlo to explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates bias toward inaccurate alignment guide-trees, employs more sophisticated substitution models during alignment and automatically utilizes information in shared insertion/deletions to help infer phylogenies. BAli-Phy also produces high-quality alignment estimates for highly divergent sequences, because it uses advanced substitution models and a realistic model of indels occurring on an (uncertain) tree. BAli-Phy can produce alignment uncertainty (AU) plots that are colored to indicate uncertain areas of the alignment.

DIALIGN

A software tool for multiple sequence alignment by combining global and local alignment features. DIALIGN composes multiple alignments from local pairwise sequence similarities. This approach is particularly useful to discover conserved functional regions in sequences that share only local homologies but are otherwise unrelated. An anchoring option allows to use external information and expert knowledge in addition to primary-sequence similarity alone. The latest version of DIALIGN optionally uses matches to the PFAM database to detect weak homologies.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

PsychoProt / Physical CHemistry Of Protein variability

Obsolete
A web app and a package to study about protein modeling, evolution and design. PsychoProt helps to (i) unveil protein structure-function relationships from experiments and from alignments that are consistent with structures according to coevolution analysis, (ii) recall global information about structural and functional features and identify hitherto unknown constraints to variation in alignments, and (iii) point at different sources of variation among related experimental datasets or between experimental and alignment-based data.

MS3ALIGN / Multi-Scale Morse-Smale Molecular-Surface Alignment tool

Obsolete
Aligns molecular surfaces based on significant protrusions on the molecular surface. A key advantage of MS3ALIGN is robust segmentation of the surface into segments that can be individually evaluated for correspondences. Furthermore, due to its purely geometric design, it is applicable to molecular surfaces arising from various sources such as the PDB and Electron-Microscopy scans. This is a key advantage over existing methods such as SurfComp, PBSalign, and PyMOL, which rely on protein sequence data and other derived scalar values such as the electrostatic potential, which are often not directly available/computable.

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.

PDBeFold

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.

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.

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..

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.

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.