1. From: Structural database resources for biological macromolecules
Figure 5. An example based on part of a real-world investigation of the molecular features of β-lactam-binding sites. One can retrieve all known β-lactam-binding sites by searching for ‘lactamase’ at scPDB. For each retrieved PDB, this webservice shows structural and chemical properties of both the binding pocket and bound ligand, plus a detailed list of protein-ligand interactions and 2D representation of it. One can then search for each of the PDB entries retrieved by scPDB at Pocketome, which will return structural and chemical information about the conserved and variable features of similar sites in other PDB entries. For a color version of this figure please visit the online article. A colour version of this figure is available at BIB online:
From: Structural database resources for biological macromolecules
Brief Bioinform. 2016;18(4): doi: /bib/bbw049
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2. From: Structural database resources for biological macromolecules
Figure 4. How PDB-derived databases for nucleic acids help highlight the structural complexity of RNA over that of DNA. For an example of protein-bound DNA (A) 100% of the base pairs are in standard Watson-Crick bonding with anti-parallel strand orientation (‘cWW’) according to NDB. This simplicity stems from the canonical B conformation adopted by this piece of DNA. But the exemplified tRNA molecule (B) has around 25% of its nucleotides in one of -in this case- 8 noncanonical pairing motifs (from NDB). This is owing to the complex 3D structure as observed in the online 3D visualization or in the simple circular representation at the RNA 3D hub. For a color version of this figure please visit the online article. A colour version of this figure is available at BIB online:
From: Structural database resources for biological macromolecules
Brief Bioinform. 2016;18(4): doi: /bib/bbw049
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3. From: Structural database resources for biological macromolecules
Figure 3. Example on using PDBFINDER II to easily retrieve the most likely secondary structures adopted by a dipeptide. This task could be achieved through a number of alternatives, but the fastest is possibly by just scanning PDBFINDER II using this set of Linux scripts and small Python program. Notice that this protocol does not require downloading any files other than the single ASCII PDBFINDER II file (ftp://ftp.cmbi.ru.nl/pub/molbio/data/pdbfinder2/PDBFIND2.TXT.gz, under 450 MB by April 2016); and that it does not require any kind of secondary structure calculations to be performed because they are already included from DSSP analysis on PDBFINDER II update. Therefore the answer is obtained in seconds. This specific example retrieves secondary structures for all Cys-Pro dipeptides in structures of the PDB, from a real-world question received from experimental collaborators. The scripts can be obtained at
From: Structural database resources for biological macromolecules
Brief Bioinform. 2016;18(4): doi: /bib/bbw049
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4. From: Structural database resources for biological macromolecules
Figure 2. An example on how to use PDBsum as a hub to structural information of the protein aquaporin-0 in this database and in related PDB-derived databases (A), with the goal of learning about the protein before setting up a molecular dynamics simulation of the protein embedded in a membrane based on the orientation stored in the OPM database (B). Panel A starts by searching for PDB ID 1SOR in PDBsum. Among many other informations, the ‘Top page’ tab for this entry has a precomputed Ramachandran plot (globe labeled 1), references listed in the PDB file (2, clicking shows relevant text and figures from the publication), species the protein sequence belongs to (3, in this case Ovis aries, sheep), a direct link to its UniProt entry (4), gene ontologies (5, indicating this is a membrane protein with transport activity), several external links (6,7, a few extended in the bottom part of the panel), two precomputed views (8,9) and a link to online 3D visualization (10). The top of this panel shows selected pictures from the ‘Protein’ and ‘Pores’ tabs, showing a planar view of the protein topology and a partially open pore identified in the asymmetric unit. Of the many links (6,7), shown are those to PDB Europe and RCSB PDB, which provide a picture of the asymmetric unit like PDBsum but also precomputed biological assemblies, in this case an homooctamer that consists of two layers of tetramers. PDB Europe and RCSB also quickly display information about the experimental conditions, structure quality (with direct reports from PROCHECK and WHATIF coming from PDBsum) and refinement statistics (which in this case can be slightly improved according to PDB_REDO). On the other hand, panel B starts by looking at the OPM entry for 1SOR, which shows how an homotetrameric unit could fit in a membrane. Using this reoriented structure one can easily set up an MD simulation of the system using Lipidbuilder or CHARMM-GUI. Finally, from annotation and wiki-based databases like Proteopedia one can quickly learn that aquaporin-0 mediates cell-cell contacts by establishing membrane junctions permeable to water. A coarse 3D model of such junctions can be made by putting together the biological assembly and membrane-embedding informations (C). For a color version of this figure please visit the online article. A colour version of this figure is available at BIB online:
From: Structural database resources for biological macromolecules
Brief Bioinform. 2016;18(4): doi: /bib/bbw049
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5. From: Structural database resources for biological macromolecules
Figure 1. The PDB data centers and the PDB-derived databases currently active as of April 2016, focus of this Briefing. A clickable version of this figure is available at
From: Structural database resources for biological macromolecules
Brief Bioinform. 2016;18(4): doi: /bib/bbw049
Brief Bioinform | © The Author Published by Oxford University Press. All rights reserved. For Permissions, please