The surface alignment of lyotropic chromonic liquid crystals can not only be planar (tangential) but also homeotropic, with self-assembled aggregates perpendicular to the substrate, as demonstrated by mapping optical retardation and by three-dimensional imaging of the director field. With time, the homeotropic nematic undergoes a transition into a tangential state. The anchoring transition is d...

Since the introduction of medical ultrasound in the 1950s, modern diagnostic ultrasound has progressed to see many major diagnostic tools come into widespread clinical use, such as B-mode imaging, color-flow imaging, and spectral Doppler. New applications, such as panoramic imaging, three-dimensional imaging, and quantitative imaging, are now beginning to be offered on some commercial ultrasoun...

Abbreviations 1D D one-dimensional; 1D structure D one-dimensional (e.g., sequence or string of secondary structure); 2D D two-dimensional; 2D structure D two-dimensional (e.g., interresidue distances); 3D D three-dimensional; 3D structure D three-dimensional (coordinates of protein structure); PDB D Protein Data Bank of experimentally determined 3D structures of proteins; SWISS-PROT D database...

The database of 3D Interacting Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how interactions occur. It also offers an overview of how similar in structure are interactions between different members of...

Secondary structure of protein, such as α-helix and βsheet, is the general three-dimensional (3D) form of local segments. It can be identified from the 3D electron cryomicroscopy (cryo-EM) density images at medium resolutions (~5-10Å). A detected β-sheet can be represented by either the voxels of β-sheet density or by many piecewise polygons to compose a rough surface. However, none of these is...

We de ned the protein inverse folding problem with an object oriented database and an empirical hydrophobic penalty function, which was derived from the number of residues around each residue in a protein three dimensional structure. Under the database management system, we compiled the known structures of proteins and the evaluation function into one functional database. In order to compare ou...

CDD, the Conserved Domain Database, is part of NCBI's Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. Pre-computed annotation is available via Entrez, and interactive search services a...

The crystal structure of a proteolytically modified form of the Escherichia coli phosphocarrier and signal transducing protein IIIglc has been determined by multiple isomorphous and molecular replacement. The model has been refined to an R-factor of 0.166 for data between 6- and 2.1-A resolution with an rms deviation of 0.020 A from ideal bond lengths and 3.2 degrees from ideal bond angles. The...

What is the significance of three-dimensional structural similarity? This fundamental question still remains unanswered in spite of advances in automatic structure comparison methods that have been made in the last few years. The answer to this question will give us a much deeper insight into the principles of protein architecture.

Proteins display a hierarchy of structural features at primary, secondary, tertiary, and higher-order levels, an organization that guides our current understanding of their biological properties and evolutionary origins. Here, we reveal a structural organization distinct from this traditional hierarchy by statistical analysis of correlated evolution between amino acids. Applied to the S1A serin...