Protein-surface structure detection software tools | Physicochemical properties data analysis
Atomistic molecular dynamics simulation is a promising technique to investigate the energetics and dynamics in the protein-surface adsorption process which is of high relevance to modern biotechnological applications. To increase the chance of success in simulating the adsorption process, favorable orientations of the protein at the surface must be determined.
Identifies regions of binding sites on the proteins. BsFinder first proceeds to a local sequence alignment then detects protein surface, and finally compares 3d structures. The software can perform four distinct analysis: prediction between two proteins, identification of sites in a protein, look for sites in an entire structure from a determined binding site, and location of all the same sites settled in a protein.
Offers a broad range of applications for fast scans of protein sequence properties in large data sets. ProFASTA enables the pipeline filtering of proteins with cell surface characteristics by analysis of output created with SignalP, TMHMM and big-PI. It also provides keyword, iso-electric point, composition and pattern scanning. This web application contains all fungal protein sequences present in the NCBI Protein database.
Performs an efficient and exhaustive conformational search of the multi-dimensional potential energy hypersurface of an oligopeptide, and locates all its low energy conformations. MOLS is a peptide conformational search tool to identify low-energy peptide structures. It also has Jmol molecule viewer and a built-in molecule builder, which may be used to create chemical compounds to be used for docking.
Assists in tracing molecular surface for meshing. TMSmesh is a system that contains two steps: (i) it computes the intersection points between the molecular Gaussian surface and the lines parallel to x-axis and (ii) the sampled surface points are connected through three algorithms to form loops, and the whole closed manifold surface is decomposed into a collection of patches enclosed by loops on the surface.
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.
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