L.I.F.E. is Beautiful

My title Life is Beautiful: An inquire on the use of small living and architectural design. I chose this title because my focus is in looking at the phases of architecture and creating beautiful and life changing architecture with the help of engineering. I aim to transform my families life by creating a small living space that does not only let earth blossom but also our family. Everyone asks me why I wanted to become an architect. If I had to sum it up, I would say I became an architect so that I could mix my love of art and engineering. Many people refer to an architect as a designer. They typically think we sit inside at desks and play with 3d printers and rendering software. Designing is a relatively small part of what an architect daily accomplishes. My family and internship experiences have greatly influenced my passion for buildings and the knowledge to understand what an architect does. For instance, my office is typically empty, because everyone is at meetings or on construction sites. Most of our work is in the construction documentation and administration phases. With my thesis I would like to understand the process an architect goes through, from design to the built. The way that I will go through the phases myself is through the design of my own tiny home on wheels. My goal is to merge elements that I have learned from my Industrial engineering minor. That would be about sustainability to make my home off the grid. This could be the use of tesla batteries, solar panels, compost toilet, etc. Another aspect is looking at the cost of materials, labor costs, and life span of those said materials. The final aspect is to look at the life span of the home and trailer, seeing how it would with stand being moved with relation to the weight of materials and its overall weight. The aspect of architecture in my project would be to look at the spatial quality, because that’s huge in roughly 700sqft. Also, to look at the zoning, transportation limits, building classification and the way those are affected by it being able to transport

SuperNatural: a searchable database of available natural compounds

Although tremendous effort has been put into synthetic libraries, most drugs on the market are still natural compounds or derivatives thereof. There are encyclopaedias of natural compounds, but the availability of these compounds is often unclear and catalogues from numerous suppliers have to be checked. To overcome these problems we have compiled a database of ∼50 000 natural compounds from different suppliers. To enable efficient identification of the desired compounds, we have implemented substructure searches with typical templates. Starting points for in silico screenings are about 2500 well-known and classified natural compounds from a compendium that we have added. Possible medical applications can be ascertained via automatic searches for similar drugs in a free conformational drug database containing WHO indications. Furthermore, we have computed about three million conformers, which are deployed to account for the flexibilities of the compounds when the 3D superposition algorithm that we have developed is used. The SuperNatural Database is publicly available at . Viewing requires the free Chime-plugin from MDL (Chime) or Java2 Runtime Environment (MView), which is also necessary for using Marvin application for chemical drawing

CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge

During the development of methods for cancer diagnosis and treatment, a vast amount of information is generated. Novel cancer target proteins have been identified and many compounds that activate or inhibit cancer-relevant target genes have been developed. This knowledge is based on an immense number of experimentally validated compound–target interactions in the literature, and excerpts from literature text mining are spread over numerous data sources. Our own analysis shows that the overlap between important existing repositories such as Comparative Toxicogenomics Database (CTD), Therapeutic Target Database (TTD), Pharmacogenomics Knowledge Base (PharmGKB) and DrugBank as well as between our own literature mining for cancer-annotated entries is surprisingly small. In order to provide an easy overview of interaction data, it is essential to integrate this information into a single, comprehensive data repository. Here, we present CancerResource, a database that integrates cancer-relevant relationships of compounds and targets from (i) our own literature mining and (ii) external resources complemented with (iii) essential experimental and supporting information on genes and cellular effects. In order to facilitate an overview of existing and supporting information, a series of novel information connections have been established. CancerResource addresses the spectrum of research on compound–target interactions in natural sciences as well as in individualized medicine; CancerResource is available at: http://bioinformatics.charite.de/cancerresource/

Representation of target-bound drugs by computed conformers: implications for conformational libraries

BACKGROUND: The increasing number of known protein structures provides valuable information about pharmaceutical targets. Drug binding sites are identifiable and suitable lead compounds can be proposed. The flexibility of ligands is a critical point for the selection of potential drugs. Since computed 3D structures of millions of compounds are available, the knowledge of their binding conformations would be a great benefit for the development of efficient screening methods. RESULTS: Integration of two public databases allowed superposition of conformers for 193 approved drugs with 5507 crystallised target-bound counterparts. The generation of 9600 drug conformers using an atomic force field was carried out to obtain an optimal coverage of the conformational space. Bioactive conformations are best described by a conformational ensemble: half of all drugs exhibit multiple active states, distributed over the entire range of the reachable energy and conformational space. A number of up to 100 conformers per drug enabled us to reproduce the bound states within a similarity threshold of 1.0 Å in 70% of all cases. This fraction rises to about 90% for smaller or average sized drugs. CONCLUSION: Single drugs adopt multiple bioactive conformations if they interact with different target proteins. Due to the structural diversity of binding sites they adopt conformations that are distributed over a broad conformational space and wide energy range. Since the majority of drugs is well represented by a predefined low number of conformers (up to 100) this procedure is a valuable method to compare compounds by three-dimensional features or for fast similarity searches starting with pharmacophores. The underlying 9600 generated drug conformers are downloadable from the Super Drug Web site [1]. All superpositions are visualised at the same source. Additional conformers (110,000) of 2400 classified WHO-drugs are also available

Oxidized Hemithioindigo Photoswitches—Influence of Oxidation State on (Photo)physical and Photochemical Properties

The photophysical and photochemical properties of sulfoxide and sulfone derivatives of hemithioindigo photoswitches are scrutinized and compared to the unoxidized parent chromophores. Oxidation results in significantly blue-shifted absorptions and mostly reduction of photochromism while thermal stabilities of individual isomers remain largely unaltered. Effective photoswitching takes place at shorter wavelengths compared to parent hemithioindigos and high isomeric yields can be obtained reversibly in the respective photostationary states. Reversible solid-state photoswitching is observed for a twisted sulfone derivative accompanied by visible color changes. These results establish oxidized hemithioindigo photoswitches as promising and versatile tools for robust light-control of molecular behavior for a wide range of applications

A semantic web ontology for small molecules and their biological targets

A wide range of data on sequences, structures, pathways, and networks of genes and gene products is available for hypothesis testing and discovery in biological and biomedical research. However, data describing the physical, chemical, and biological properties of small molecules have not been well-integrated with these resources. Semantically rich representations of chemical data, combined with Semantic Web technologies, have the potential to enable the integration of small molecule and biomolecular data resources, expanding the scope and power of biomedical and pharmacological research. We employed the Semantic Web technologies Resource Description Framework (RDF) and Web Ontology Language (OWL) to generate a Small Molecule Ontology (SMO) that represents concepts and provides unique identifiers for biologically relevant properties of small molecules and their interactions with biomolecules, such as proteins. We instanced SMO using data from three public data sources, i.e., DrugBank, PubChem and Urn Prot. and converted to RDF triples. Evaluation of SMO by use of predetermined competency questions implemented as SPARQL queries demonstrated that data from chemical and biomolecular data sources were effectively represented and that useful knowledge can be extracted. These results illustrate the potential of Semantic Web technologies in chemical, biological, and pharmacological research and in drug discovery