An online tool that locates and measures pockets and voids on 3D protein structures. CASTp includes annotated functional information of specific residues on the protein structure. The annotations are derived from the Protein Data Bank (PDB), Swiss-Prot, as well as Online Mendelian Inheritance in Man (OMIM), the latter contains information on the variant single nucleotide polymorphisms (SNPs) that are known to cause disease.
Generates molecular surfaces and gaps between surfaces from 3D coordinates supplied in a PDB-format file. The gap regions can correspond to the voids between two or more molecules, or to the internal cavities and surface grooves within a single molecule. The program is particularly useful in clearly delineating the regions of the active site of a protein. It can also generate 3D contour surfaces of the density distributions of any set of 3D data points.
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).
A highly versatile and easy-to-use tool for cavity prospection and spatial characterization. KVFinder is a geometrical-based method that has an innovative customization of the search space. It presents novel usability features, granting full customizable and highly detailed cavity prospection on proteins, alongside with a friendly graphical interface.
Finds protein cavities throughout Molecular Dynamics (MD) simulation trajectories. trj_cavity can analyse the solvent occupancy of the cavities identified. This tool is implemented within the GROMACS framework for the rapid identification and characterization of cavities detected within MD trajectories. It is also optimized for usability and computational efficiency and is applicable to the time-dependent analysis of any cavity topology, and optional specialized descriptors can be used to characterize, protein channels.
Molecular cavities, which include voids and channels, are critical for molecular function. BetaCavityWeb computes these cavities for a given molecular structure and a given spherical probe, and reports their geometrical properties: volume, boundary area, buried area, etc. The server's algorithms are based on the Voronoi diagram of atoms and its derivative construct: the beta-complex.
Calculates a number of bioinformatic and biophysical features of a protein structure file. MarkUs is a server for the analysis and comparison of the structural and functional properties of proteins. It also determines whether a function is consistent with the properties of the query structure itself and identifies function-determining properties that will guide experimental validation.