Secondary structure detection software tools | Protein data analysis
Protein secondary structure refers to the three-dimensional form of local segments of proteins, such as alpha helices and beta sheets. Secondary structure is defined by the amino-acid sequence of the protein, and as such can be predicted using specific computational algorithms. Most secondary structure prediction software use a combination of protein evolutionary information and structure homology. Accurate secondary-structure prediction is a key element in the prediction of tertiary structure.
Computes RNA base reactivity scores. icSHAPE proposes a ten-steps pipeline that starts from polymerase chain reactions (PCR) removal to lastly produces UCSC tracks of the results. This program aims to measure RNA structural profiles of polyadenylated transcripts in mouse embryonic stem cells (mESCs). This approach can be employed to any ex vivo preparation of RNA with slight modifications.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Provides a suite of methods important for the prediction of protein structural and functional features. predictProtein is a web server that incorporates over 30 tools. This software searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function. It can help when little is known about the protein in question. For medium-to-high throughput analyses, downloadable software packages and the PredictProtein Machine Image (PPMI) are available.
Generates optimized potential for efficient protein structure prediction (OPEP) files. OPEP Files Generator is a web application that combines energetic and structural accuracy and chemical specificity. It allows studying single protein properties, DNA/RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. It can be useful for systems required to be used for ART, MD, REMS, ST, MUPHY, MD/DRIVER software packages.
Predicts 3D structure of a protein sequence. Phyre is a web application that investigates known homologues, builds a hidden Markov model (HMM) of the targeted sequence based on the detected homologues and scans it against a database of HMMs of known protein structures. It also provides advanced features such as a batch submission of a large number of protein sequences for modelling or Phyre Investigator, that allows users to analyze model quality, function and effects of mutations.
Allows protein sequence analysis. ANTHEPROT is able to interactively couple multiple alignments with secondary structure predictions. It can submit tasks on a remote server and retrieve data from a remote Web server. This tool is a complete solution for Intranet protein sequence analysis for universities, biological research institutes or biomedical companies. It permits users to integrate secondary structure predictions within multiple alignment and full interactive editing of alignments.
A protein secondary structure prediction server. JPred incorporates the Jnet algorithm in order to make more accurate predictions. In addition to protein secondary structure, JPred also makes predictions on solvent accessibility and coiled-coil regions.
Aggregates a number of protein annotation tools and provides services or software to allow users to perform truly scalable biological analyses. PSIPRED offers to the user the possibility to choose the method wanted to conduct the analysis. It proposes the following sequence and structure annotation methods: PSIPRED, GenTHREADER, pGenTHREADER, pDomTHREADER, MEMSAT-SVM/MEMSAT3, MEMPACK, BioSerf, MetSite, HSPred, DISOPRED2, DomPred and FFPred. The tool permits to select any number of appropriate simultaneous analyses across all the applicable methods and easily explore results.
Provides improved automated tools for protein structure prediction and analysis using consensus. Pcons.net is an online application containing features for producing a model of a protein sequence. It allows users to: (1) find different templates; (2) align the template to the query sequence; (3) build a 3D structure based on the alignment; and (4) assesses the quality of the model.
Determines protein secondary structure (SS). Porter leans on ensembles of bidirectional recurrent neural networks (BRNN). It is useful for generating eight-state SS predictions. This tool consists of two similar cascaded stages and was trained on a set containing more than 15 500 proteins and was evaluated on a set of over 3 000 proteins.
Provides access to a variety of public and in-house bioinformatics tools. The MPI Bioinformatics Toolkit integrates a selected set of most useful methods for the analysis of protein sequences and structures. It offers more of 50 interconnected tools, so that the results of one tool can be forwarded to other tools. It also includes a useful platform for teaching bioinformatic enquiry to students in the life sciences.
Consists of a suite of webservers for the prediction of protein structural features. Distill is an online server that assists users to annotate protein sequences through several methods. It allows prediction of protein structures for the case in which some homology to the protein data bank (PDB) is detectable. Moreover, its online interface is able to receive multiple queries in FASTA format.
Provides a software tool for secondary structure assignment from atomic resolution protein structures. STRIDE implements a knowledge-based algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignments in maximal agreement with crystallographers' designations. The STRIDE web server provides access to this tool and allows visualization of the secondary structure, as well as contact and Ramachandran maps for any file uploaded by the user with atomic coordinates in the Protein Data Bank (PDB) format. A searchable database of STRIDE assignments for the latest PDB release is also provided as well as a link to the source code to use STRIDE as a stand-alone program.
Predicts NO Regular Secondary structure (NORS) regions publicly accessible. norsp extracts the secondary structure and evaluate the presence of transmembrane helices and coiled-coil in proteins. The application can be applied to help crystallographers to detect presence of NORS regions in proteins. Besides it can be useful for biologists interested in protein structure–function relationship to explore if protein–protein interaction sites coincide with NORS regions.
Determines tertiary protein structure. TOUCHSTONE is based on a simplified lattice representation of the C alpha, C beta, and center of side group of protein chains. It utilizes multiple sequence alignments to increase the prediction accuracy of secondary structures. This tool represents a lattice description that has a high geometric fidelity. It allows assembly and optimization of tertiary structures when threading information are available.
Assists users in standardizing secondary structure assignment. DSSP calculates DSSP entries from PDB entries. It also includes a resource of secondary structure assignments for protein entries in the Protein Data Bank (PDB). This application does not predict secondary structure.
Predicts protein secondary structure using a combination of protein evolutionary information (sequence homology) coupled to homologous protein's secondary structure (structure homology). The application assigns secondary structures according three different classes (i) helix, (ii) strand and (iii) the rest. The software can also be run as a web application through the SCRATCH web server.
Provides 3D models. SAM-T08 is a protein structure prediction server that offers a large number of intermediate results, which are often interesting in their own right: multiple sequence alignments (MSAs) of putative homologs, prediction of local structure features, lists of potential templates of known structure, alignments to templates and residue–residue contact predictions. This server has been validated as part of the CASP8 assessment of structure prediction.
Predicts ß-turns in a protein from the amino acid sequence. It allows the user to predict turns in a protein using existing statistical algorithms, to predict the type of ß-turn such as Type I, I', II, II', VI, VIII and non-specific i.e., advanced prediction and to predict the consensus ß-turn in a protein.
Topics (10): Protein structure analysis, Staphylococcus aureus, Escherichia coli, Human alphaherpesvirus 1, Human alphaherpesvirus 2, Candida parapsilosis, Trichophyton mentagrophytes, Trichophyton rubrum, Homo sapiens, Drug-Related Side Effects and Adverse Reactions