Macromolecular structures: Quality assessment and biological interpretation

MetalPDB: a database of metal sites in biological macromolecular structures

We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Mi...

Biological Nano-crystallization ▶Macromolecular Crystallization Using Nano- volumes Biological Photonic Structures

Macromolecular structures without crystals.

E lectron microscopy has many attractive capabilities as a tool for experimentally visualizing the structures of biological cells and macromolecules. Particles can be imaged while freely suspended in biochemically ‘‘native’’ buffers, and electrons can be focused to resolutions exceeding anything that a biochemist’s heart might desire. To be sure, biological electron microscopy also is subject t...

Deposition of macromolecular structures.

Macromolecular structures are being determined at an increasing rate, and are of interest to a wide diversity of researchers. Depositing a macromolecular structure with the Protein Data Bank makes it readily available to the community. Accuracy, consistency and machine-readability of the data are essential, as are clear indications of quality, and sufficient information to allow non-experimenta...

Fractal Dimensions of Macromolecular Structures

Quantifying the properties of macromolecules is a prerequisite for understanding their roles in biochemical processes. One of the less-explored geometric features of macromolecules is molecular surface irregularity, or 'roughness', which can be measured in terms of fractal dimension (D). In this study, we demonstrate that surface roughness correlates with ligand binding potential. We quantified...