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POVME / POcket Volume Measurer
Allows users to extract actionable information from ensembles of protein structures. POVME is a binding pocket analysis software that performs pocket selection for ensemble docking and provides outputs suitable for quantitative analysis. The software includes several features such as chemical coloring scheme for binding pockets and the option to define pocket regions based on the position of a ligand molecule. By connecting molecular dynamics (MD) simulations, pocket shapes and ligand binding, it aims to make the field of drug design more open to machine learning techniques.
A program suite to analyse and visualize the atomic packing of protein structures. Voronoia is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. Voronoia is also targeted to detect locations of putative internal water or binding sites for ligands. Accordingly, Voronoia is beneficial for a broad range of protein structure approaches.
AVP / Another Void Program
A method for the analysis of voids in proteins and packing quality in a single united program. Traditionally been analysed using different approaches, but in reality they are extremes of the same phenomenon - imperfect packing of atoms in the inside of a protein. AVP adapts is a grid-based void-finding method which allows detection of voids of any size and may therefore also be used to assess packing quality. This is achieved by using two probes: one to delimit the solvent accessible regions, the second to identify voids. This allows you to use very small or zero sized void probes without 'leakage' of the void into the bulk solvent.
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.
Allows for a rapid and fully automated analysis of molecular structures. The software calculates the surface area and the volume of molecular structures, as well as the volume of molecular cavities. The surface area facility can be used to calculate the solvent-exposed surface area of a molecule or the contact area between two molecules. The volume algorithm can be used to predict not only the space occupied by any molecular structure, but also the volume of cavities, such as tunnels or clefts. VolArea is as a plug-in of the widely distributed software Visual Molecular Dynamics (VMD).
A program for detection of cavities in macromolecular structures. It uses an algorithm that makes it possible to detect even certain types of cavities that are connected to "the outside world". Three different types of cavity can be handled by VOIDOO: Vanderwaals cavities (the complement of the molecular Vanderwaals surface), probe-accessible cavities (the cavity volume that can be occupied by the centres of probe atoms) and MS-like probe-occupied cavities (the volume that can be occupied by probe atoms, i.e. including their radii).
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