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.
Calculates the atomic accessible surface defined by rolling a probe of given size around a van der Waals surface. Naccess is able to calculate the atomic and residue accessibilities for both proteins and nucleic acids. The tool can be used for up to 20000 atoms, and allows the variation of the probe size and atomic radii by the user. It works by taking thin Z-slices through the molecule and calculating the exposed arc lengths for each atom in each slice, and then summing the arc lengths to the final area over all z-values.
Allows prediction of secondary structure, accessible surface area and dihedral angles. SPINE-X is a secondary structure prediction method consisting of six steps of iterative prediction of secondary structure (SS), real-value residue solvent accessibility (RSA), and dihedral angles. The software can produce a distribution of three secondary structure states that is very close to the native distribution.
Predicts the relative surface accessibility of an amino acid and simultaneously predicts the reliability for each prediction, in the form of a Z-score. NetSurfP is composed of two neural network ensembles: the primary predicts secondary structure and have two outputs corresponding to buried or exposed; the secondary predicts the relative surface exposure of the individual amino acid residues. The tool is able to assign a reliability score to each surface accessibility prediction as an inherent part of the training process.
A tool to predict changes in protein stability upon point mutations. The prediction model uses amino acid-atom potentials and torsion angle distribution to assess the amino acid environment of the mutation site. Additionally, the prediction model can distinguish the amino acid environment using its solvent accessibility and secondary structure specificity.
A regression-based method for secondary structure prediction that utilizes predicted solvent exposure of an amino acid residue as an additional attribute describing its environment. SABLE follows the 2-stage protocol of Rost and Sander, with a number of Elman-type recurrent neural networks (NNs) combined into a consensus predictor.
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.