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.
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.
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.
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.
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.
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.
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.
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.