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PISA / Protein Data Bank in Europe Proteins Interfaces Structures and Assemblies
Retrieves pre-calculated results for the whole Protein Data Bank (PDB) archive. PISA is an interactive tool for the exploration of macromolecular interfaces. It calculates results interactively for structures uploaded as PDB or mmCIF files. These calculated results include: (i) structural and chemical properties of macromolecular surfaces and interfaces and (ii) probable quaternary structures (assemblies), their structural and chemical properties and probable dissociation pattern.
A self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption. ProtPOS searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies.
RKHS / Reproducing Kernel Hilbert Space
Allows to automatically construct multi-dimensional potential energy surfaces (PESs). RKHS is a toolkit for constructing multi-dimensional PESs given a grid of training data from ab initio calculations or empirical expressions. The software has no dependencies, does not require a complex build system and can be freely modified and included in other projects. It supports any number of dimensions and can also be used for general machine learning applications, e.g. for the interpolation of D-dimensional functions.
ESES / Eulerian solvent excluded surface
Constructs solvent excluded surfaces (SESs) in the Cartesian representation. ESES robustly generates meshes readily available for being used in solving the Poisson–Boltzmann (PB) or Poisson–Nernst–Planck (PNP) type of equations in the Cartesian grid. The software is validated by a large number of benchmark tests, including morphological visualization, electrostatic solvation analysis, surface area and enclosed volume calculations, and topological feature analysis and characterization.
Metadyn View
Provides a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. Metadyn View is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies, free energy differences and data/image export.
Finds functional sites on protein structures. HotPatch finds surface patches of unusual physicochemical properties on protein structures, and estimates the patches’ probability of overlapping functional sites. First, the program computes, for each patch, a statistical estimator representing the probability that the patch overlaps a functional site. Second, it is optimized to predict very specific patches, where specificity is defined as the fraction of residues in the predicted region that are functional. Third, HotPatch treats oligomers in their biologically relevant quaternary structure. Fourth, the approach is general: the property analyzed can be any smoothly varying local property of proteins, such as hydrophobicity, electrostatic potential, or a combination via a neural network.
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