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.
Predicts protein cavity and allows functional analyses. CavityPlus can recognize cavities on protein surfaces. It can be employed for: pharmacophore modelling, allosteric site identification, and covalent ligand-binding ability prediction for a given cavity. This tool enables the discovery of novel binding sites for designing covalent allosteric ligands. It is useful for many aspects of drug design and discovery, such as target selection and identification, virtual screening or de novo drug design.
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.
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.
Computes the void parts of the proteins, i.e. cavities, channels and pockets. The present approach is a variant of the alpha shapes method, with the advantage of taking into account the size and the shape of the ligand.
Implements an algorithm which uses Euclidean distance transform (EDT) to convert the target protein structure into a 3D gray-scale image, where depths of atoms in the protein can be conveniently and precisely derived from the minimum distance of the pixels to the surface of the protein. EDTSurf allows to construct triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface). EDTSurf also identifies cavities which are inside of macromolecules. Furthermore, EDTSurf has been extended to calculate atom depth and residue depth to solvent-accessible surface.
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.
Recognizes molecular voids in the van der Waals surface or the Lee-Richards (solvent accessible) surface and computes their mass properties such the volume and the boundary area. Because BetaVoid is based on the beta-complex, its correctness and efficiency are mathematically guaranteed.
A toolkit for identifying pockets, cavities and channels of protein structures. The toolkit was developed in PERL programming language and includes “PoreID” for pore identification, “PoreTrace” for pore axes determination and “GateOpen” for opening the gate between neighboring pores. “PoreID” is a grid-based method that avoids orientation dependency of the results. It targets all kinds of pores (pockets, cavities and channels) and is automatic so that only the PDB file of the target protein has to be specified by the user.
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.
A computer program supporting the visualization of voids. PrinCCes includes a novel algorithm for the decomposition of the entire void volume of the protein or protein complex to individual entities. The decomposition is based on continuity. An individual void is defined by uninterrupted extension in space: a spherical probe can freely move between any two internal locations of a continuous void. Continuous voids are detected irrespective of their topological complexity, they may contain any number of holes and bifurcations. The voids of a protein can be visualized one by one or in combinations as triangulated surfaces.
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).
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.
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