261 research outputs found
Representation and Misrepresentation in Biomolecular Science
Biological molecules are too small for direct imaging, so synthetic images are used for study and presentation of molecular structure. Three basic types of images are widely used, using different fictional elements to display different aspects of the structure: bond diagrams represent each covalent bond as a single line; spacefilling diagrams represent each atom as a sphere; and ribbon diagrams are schematic representations of the molecular topology. The widespread, and nearly exclusive, use of these three types of diagrams has influenced the course of biomolecular research and the perception of molecules in the popular media
MOLECULE OF THE MONTH:
Our diet includes a wide variety of different molecules. Many of these molecules are broken down completely and used to generate the metabolic energy that powers our cells. Others are disassembled piece-by-piece and recycled to build our own proteins and nucleic acids. The ones that are left over are broken down and discarded. Xanthine oxidoreductase, shown here from PDB entry 1fo4, is the last stop for extra purine nucleotides (ATP and GTP) in our cells. Purines are broken down in several steps, ultimately yielding uric acid, which is excreted from the body. About the RCSB PDB Molecule of the Month Using selected molecules from the PDB archive, each feature includes an introduction to the structure and function of the molecule, a discussion of its relevance to human health and welfare, and suggestions for viewing and accessing further details. The RCSB PDB Molecule of the Month is read by students, teachers, and scientists worldwide at www.pdb.org
Visualising microorganisms from molecules to cells
10 images from FEMS articles have been selected to show the diversity of visualisation used in microbiolog
Filling in the Gaps: Artistic License in Education and Outreach
Conscious and careful application of artistic license is an essential part of the creation of scientific illustrations for research, education, and science outreach
Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves a community of users with diverse backgrounds and interests. In addition to processing, archiving and distributing structural data, it also develops educational resources and materials to enable people to utilize PDB data and to further a structural view of biology
Redox-Based Probes for Protein Tyrosine Phosphatases
No AbstractPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/83769/1/4423_ftp.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/83769/2/anie_201007871_sm_miscellaneous_information.pd
Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes
The results from reiterated docking experiments may be used to evaluate an empirical vibrational entropy of binding in ligand–protein complexes. We have tested several methods for evaluating the vibrational contribution to binding of 22 nucleotide analogues to the enzyme APS reductase. These include two cluster size methods that measure the probability of finding a particular conformation, a method that estimates the extent of the local energetic well by looking at the scatter of conformations within clustered results, and an RMSD-based method that uses the overall scatter and clustering of all conformations. We have also directly characterized the local energy landscape by randomly sampling around docked conformations. The simple cluster size method shows the best performance, improving the identification of correct conformations in multiple docking experiments. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/60220/1/20936_ftp.pd
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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
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