A series of PDB-related databanks for everyday needs

Abstract

We present a series of databanks (http://swift.cmbi.ru.nl/gv/facilities/) that hold information that is computationally derived from Protein Data Bank (PDB) entries and that might augment macromolecular structure studies. These derived databanks run parallel to the PDB, i.e. they have one entry per PDB entry. Several of the well-established databanks such as HSSP, PDBREPORT and PDB_REDO have been updated and/or improved. The software that creates the DSSP databank, for example, has been rewritten to better cope with π-helices. A large number of databanks have been added to aid computational structural biology; some examples are lists of residues that make crystal contacts, lists of contacting residues using a series of contact definitions or lists of residue accessibilities. PDB files are not the optimal presentation of the underlying data for many studies. We therefore made a series of databanks that hold PDB files in an easier to use or more consistent representation. The BDB databank holds X-ray PDB files with consistently represented B-factors. We also added several visualization tools to aid the users of our databanks.

2′-Deoxyribosyltransferase from Bacillus psychrosaccharolyticus: A Mesophilic-Like Biocatalyst for the Synthesis of Modified Nucleosides from a Psychrotolerant Bacterium

“…Analysis of the interfacial surfaces was done with the PISA server [31]. Analysis of the secondary structure was done with the DSSP (Dictionary of Secondary Structure of Proteins) server [58]. Stereochemistry validation was done with the Phenix MolProbity tool plus de wwPDB Deposition server.…”

TAPO: A combined method for the identification of tandem repeats in protein structures

“…Data Tables S1 and S2). For this purpose, we calculated the fractional Accessible Surface Area (fASA) of the residues, using the DSSP package for ASA [42,43] and dividing the ASA for a given residue by the ASA for that residue in an extended Ala-Xaa-Ala tripeptide. The interior side-chains have fASA equal to or less than 0.10; otherwise, it is considered to be solvent-exposed.…”

Structural Dynamics is a Determinant of the Functional Significance of Missense Variants

“…MBS (29) was computed with code adapted from ref. 37, and SASAs were computed using the DSSP program (31). The SEQ features based on the PSIC score (38) were extracted from PolyPhen-2 (2, 32).…”

“…To explore whether features derived from structural dynamics, referred to as dynamical (DYN) features, can help improve the overall accuracy of variant classification, we considered the following features: (i) gaussian network model (GNM)-based meansquare fluctuations (MSF) of residues, where minima indicate the sites that potentially act as hinges for supporting the protein's mechanics; (ii) the propensity of residues to act as sensors or as effectors of allosteric signals (27) based on perturbation-response scanning (PRS) analysis (28) of their ability to sense or transmit local perturbations; (iii) the mechanical bridging score (MBS) (29), which quantifies the role of each residue in maintaining the stability of the protein modeled as an anisotropic network model (ANM); and (iv) the mechanical stiffness associated with each residue, as computed by MechStiff (30). In addition to these features, we included a structural property that is a major determinant of conformational flexibility, the solvent-accessible surface area (SASA), computed using the DSSP program (31). See SI Appendix, Supplementary Methods for more details on the physical meaning and origin of these features.…”