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OPEP Files Generator / Optimized Potential for Efficient protein structure Prediction Files Generator
New
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.
ANTHEPROT
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.
PSIPRED / Predict Secondary Structure
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.
STRIDE
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.
ProteinsPlus
Allows users to access and preprocess structural data for all kinds of life science research, and gives an immediate visual impression of the overall protein structure and contained ligand molecules. ProteinPlus contains a server for special interest to life scientists with an occasional need to work with protein structures thanks to six services addressing the most important tasks at the beginning of structure analysis (Protoss; PoseView; EDIA; SIENA; DoGSiteScorer; HyPPI). Users can choose an application service of interest, set additional tool configurations and start the calculation.
ESPript / Easy Sequencing in PostScript
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.
FELLS / Fast Estimator of Latent Local Structure
Aims to visualize structural features from the protein sequence. FELLS provides disorder, aggregation and low complexity predictions as well as estimated local propensities including amphipathicity. A fast estimator of secondary structure (FESS) is also trained to provide a fast response. The calculations required for FELLS are extremely fast and suited for large-scale analysis while providing a detailed analysis of difficult cases. FELLS web server is freely accessible online. The server also exposes RESTful functionality allowing programmatic prediction requests. Furthermore, an executable version can be downloaded for local use.
PSSpred / Protein Secondary Structure PREDiction
A neural network training algorithm for accurate protein secondary structure prediction. PSSpred collects multiple sequence alignments using PSI-BLAST. Amino-acid frequence and log-odds data with Henikoff weights are used to train secondary structure, separately, based on the Rumelhart error backpropagation method. The final secondary structure prediction result is a combination of 7 neural network predictors from different profile data and parameters.
conSSert / Consensus Secondary Structure Prediction
A consensus secondary structure prediction method, based on support vector machines (SVM) and providing exceptional accuracy for the prediction of beta-strands with QE accuracy of over 0.82 and a Q2-EH of 0.86. conSSert uses as input probabilities for the three types of secondary structure (helix, strand, and coil) that are predicted by four top performing methods: PSSpred, PSIPRED, SPINE-X, and RAPTOR. conSSert was trained/tested using 4261 protein chains from PDBSelect25, and 8632 chains from PISCES. Further validation was performed using targets from CASP9, CASP10, and CASP11.
PCASSO / Protein C-Alpha Secondary Structure Output
Assigns protein secondary structure elements (SSEs). PCASSO is based on the well-known random forest (RF) approach. It can be used in network analysis through SSE clustering, high-throughput SSE studies, universal SSE assignments, SSE-based alignments, renormalization of Go-like models for intrinsically disordered proteins. The tool allows the analysis of coarse-grained simulation models that do not incorporate any native contact information.
HAAD / Hydrogen Atom Addition
Implements a computer algorithm for constructing hydrogen atoms from protein heavy-atom structures. In HAAD, the hydrogen is added by minimizing atomic overlap and encouraging hydrogen bonding. The method is built on the basic theory of orbital hybridization, followed by the optimization of steric repulsion and electrostatic interactions. HAAD constructs H-atoms in protein structures with an appreciable accuracy. In three independent tests based on experimental data from ultra-high-resolution X-ray structures, neutron diffraction experiments, and NOE proton-proton distance restraint data, the overall accuracy of the hydrogen positioning by HAAD is consistently higher than that of other methods used for hydrogen construction. The software is available online or can be downloaded for local use.
Mocapy++
Constructs probabilistic models of biomolecular structure, due to its support for directional statistics. Mocapy++ is a toolkit for parameter learning and inference in dynamic Bayesian networks (DBNs). It supports a wide range of DBN architectures and probability distributions, including distributions from directional statistics (the statistics of angles, directions and orientations). The tool is suitable for the Kent distribution on the sphere and the bivariate von Mises distribution on the torus.
PCI-SS / Parallel Cascade Identification -Based Protein Secondary Structure Site Prediction Server
Provides both human- and machine-readable interfaces to Parallel Cascade Identification (PCI)-based protein secondary structure prediction. PCI-SS contains two interfaces helping users to realize their prediction: (1) the human interface allows to download the structure prediction in XML format for easy parsing; (2) the machine-invocable Simple Object Access Protocol (SOAP) allows the language-independent creation of custom application-specific programs which can invoke PCI-SS remotely.
Protein Beta-Sheet Structure Prediction
Predicts protein β-sheet structure. Protein Beta-Sheet Structure Prediction consist in a dynamic programing based algorithm for protein β-strands alignment. The software main features are (i) suggestion of new alignment scores, (ii) considering the contact map scores as prior knowledge, (iii) considering the trade-off between the scores, (iv) considering different gap penalties, (v) extending the dynamic programming approach to work with prior knowledge and (vi) reducing the alignment time complexity.
PreSSAPro
Provides predictions of secondary structures starting from the amino acid sequence of a given protein. PreSSAPro uses the residue propensity values in different secondary structural types determined from the ratio of the residue’s frequency of occurrence in helices, beta-strand and coil versus its frequency of occurrence. It can be used to investigate protein structure in consideration of the protein capability to strongly modify its architecture depending on the environmental conditions.
NIAS-Server / Neighbors Influence of Amino Acids and Secondary Structures
A server to help the analysis of the conformational preferences of amino acid residues in proteins. NIAS is a web-based tool used to extract information about conformational preferences of amino acid residues and secondary structures in experimental-determined protein templates. This information is useful, for example, to characterize folds and local motifs in proteins, molecular folding, and can help the solution of complex problems such as protein structure prediction, protein design, among others.
SOPMA / Self-Optimized Prediction from Multiple Alignment
Predicts protein secondary structure by consensus prediction from multiple alignments. SOPMA correctly predicts 69.5% of amino acids for a three-state description of the secondary structure (a-helix. (3-sheet and coil) in a whole database containing 126 chains of non-homologous (less than 25% identity) proteins. It constitutes a valuable alternative to the neural networks-based methods, which can be biased by a dependence between the learning and the training sets of proteins.
ASSP / Assignment of Secondary Structures in Proteins
Path traversed by the CA atoms is used to devise a new method, ASSP (Assignment of Secondary Structure in Proteins), for the identification of secondary structure elements in proteins. ASSP is an extension of our in-house program HELANAL-Plus. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of geometrical parameters and depending on their values, the stretches can be classified into different SSEs, viz. α-helices, 310, π, PPII helices and strands. ASSP can provide a better understanding of the finer nuances of protein secondary structures. The web server version of ASSP uses JmolApplet to display the protein molecules. ASSP is available as a standalone program as well as web server
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