ProFunc: a server for predicting protein function from 3D structure

ProFunc () is a web server for predicting the likely function of proteins whose 3D structure is known but whose function is not. Users submit the coordinates of their structure to the server in PDB format. ProFunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. A summary of the analyses provides an at-a-glance view of what each of the different methods has found. More detailed results are available on separate pages. Often where one method has failed to find anything useful another may be more forthcoming. The server is likely to be of most use in structural genomics where a large proportion of the proteins whose structures are solved are of hypothetical proteins of unknown function. However, it may also find use in a comparative analysis of members of large protein families. It provides a convenient compendium of sequence and structural information that often hold vital functional clues to be followed up experimentally

MGOS: A library for molecular geometry and its operating system

The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present "Molecular Geometry (MG)'' as a theoretical framework accompanied by "MG Operating System (MGOS)'' which consists of callable functions implementing the MG theory. MG allows researchers to model complicated molecular structure problems in terms of elementary yet standard notions of volume, area, etc. and MGOS frees them from the hard and tedious task of developing/implementing geometric algorithms so that they can focus more on their primary research issues. MG facilitates simpler modeling of molecular structure problems; MGOS functions can be conveniently embedded in application programs for the efficient and accurate solution of geometric queries involving atomic arrangements. The use of MGOS in problems involving spherical entities is akin to the use of math libraries in general purpose programming languages in science and engineering. (C) 2019 The Author(s). Published by Elsevier B.V

A Broadband Left-Handed Metamaterial Microstrip Antenna with Double-Fractal Layers

This paper proposes a microstrip patch antenna based on the left-handed metamaterial concept, using planar periodic geometry, which results in improved characteristics. This periodic geometry is derived from fractal shapes, which have been widely used in antenna engineering. The metamaterial property was obtained as a result of the double-fractal structure on both the upper and the bottom sides of the antenna. The final structure has been optimized to enhance bandwidth, gain, and radiation characteristics of the microstrip antenna. This combination significantly improved antenna performance; our design could support an ultrawide bandwidth ranging from 4.1 to 19.4 GHz, demonstrating higher gain with an average value of 6 dBi over the frequency range and a peak of 10.9 dBi and a radiation capability directed in the horizontal plane of the antenna

Structure of SAICAR synthase from Thermotoga maritima at 2.2 Å reveals an unusual covalent dimer

The crystal structure of phophoribosylaminoimidazole-succinocarboxamide or SAICAR synthase from T. maritima at 2.2 Å revealed an unusual covalent dimer

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.

FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme's sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering ~1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms. The resource is freely available through a web interface: www.ebi.ac.uk/thorton-srv/databases/FunTree