منابع مشابه
Personalization of structural PDB files.
PDB format is most commonly applied by various programs to define three-dimensional structure of biomolecules. However, the programs often use different versions of the format. Thus far, no comprehensive solution for unifying the PDB formats has been developed. Here we present an open-source, Python-based tool called PDBinout for processing and conversion of various versions of PDB file format ...
متن کاملAnnotating PDB files with scene information.
We have implemented extensions to the Brookhaven Protein Data Bank (PDB) file format for incorporating scene information such as viewing parameters, additional molecular information (e.g., van der Waals radii and atom colors), and user-defined graphics. These extensions were made in conformance with the PDB standard and provide sufficient information to render the scene in various styles such a...
متن کاملBDB: databank of PDB files with consistent B-factors.
Protein structures available from the PDB contain for each atom the coordinates, the occupancy and the B-factor that indicates the mobility of the atom. The values that should represent B-factors can relate to atomic motions in different ways. We present here a databank in which all B-factors have been converted to the one, homogeneous representation that is most useful for protein engineering ...
متن کاملPDBToSDF: Create ligand structure files from PDB file
Protein Data Bank (PDB) file contains atomic data for protein and ligand in protein-ligand complexes. Structure data file (SDF) contains data for atoms, bonds, connectivity and coordinates of molecule for ligands. We describe PDBToSDF as a tool to separate the ligand data from pdb file for the calculation of ligand properties like molecular weight, number of hydrogen bond acceptors, hydrogen bo...
متن کاملPDBsum: Structural summaries of PDB entries
PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand and protein-DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users ...
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ژورنال
عنوان ژورنال: Acta Biochimica Polonica
سال: 2013
ISSN: 1734-154X,0001-527X
DOI: 10.18388/abp.2013_2025