The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine

Pre-calculated protein structure alignments at the RCSB PDB website: Fig. 1.

Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

The Protein Data Bank (PDB) is the central worldwide repository for three-dimensional (3D) structure data of biological macromolecules. The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data. The re-engineered site is currently in public beta test at http://pdbbeta.rcsb.org. The new site expands the functionality of the existing site by providing structure data in greater detail and uniformity, improved query and enhanced analysis tools. A new key feature is the integration and searchability of data from over 20 other sources covering genomic, proteomic and disease relationships. The current capabilities of the re-engineered site, which will become the RCSB production site at http://www.pdb.org in late 2005, are described

Cosmic Rays and the Search for a Lorentz Invariance Violation

This is an introductory review about the on-going search for a signal of Lorentz Invariance Violation (LIV) in cosmic rays. We first summarise basic aspects of cosmic rays, focusing on rays of ultra high energy (UHECRs). We discuss the Greisen-Zatsepin-Kuz'min (GZK) energy cutoff for cosmic protons, which is predicted due to photopion production in the Cosmic Microwave Background (CMB). This is a process of modest energy in the proton rest frame. It can be investigated to a high precision in the laboratory, if Lorentz transformations apply even at factors $\gamma \sim O(10^{11})$. For heavier nuclei the energy attenuation is even faster due to photo-disintegration, again if this process is Lorentz invariant. Hence the viability of Lorentz symmetry up to tremendous gamma-factors - far beyond accelerator tests - is a central issue. Next we comment on conceptual aspects of Lorentz Invariance and the possibility of its spontaneous breaking. This could lead to slightly particle dependent ``Maximal Attainable Velocities''. We discuss their effect in decays, Cerenkov radiation, the GZK cutoff and neutrino oscillation in cosmic rays. We also review the search for LIV in cosmic gamma-rays. For multi TeV gamma-rays we possibly encounter another puzzle related to the transparency of the CMB, similar to the GZK cutoff. The photons emitted in a Gamma Ray Burst occur at lower energies, but their very long path provides access to information not far from the Planck scale. No LIV has been observed so far. However, even extremely tiny LIV effects could change the predictions for cosmic ray physics drastically. An Appendix is devoted to the recent hypothesis by the Pierre Auger Collaboration, which identifies nearby Active Galactic Nuclei - or objects next to them - as probable UHECR sources.Comment: 81 pages, 15 figures, some points extended and improved, references adde

Pre-calculated protein structure alignments at the RCSB PDB website

Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user