TarFisDock is a web-based tool for automating the procedure of searching for small molecule–protein interactions over a large repertoire of protein structures. It offers PDTD (potential drug target database), a target database containing 698 protein structures covering 15 therapeutic areas and a reverse ligand–protein docking program. In contrast to conventional ligand–protein docking, reverse ligand–protein docking aims to seek potential protein targets by screening an appropriate protein database. The input file of this web server is the small molecule to be tested, in standard mol2 format; TarFisDock then searches for possible binding proteins for the given small molecule by use of a docking approach. The ligand–protein interaction energy terms of the program DOCK are adopted for ranking the proteins. To test the reliability of the TarFisDock server, we searched the PDTD for putative binding proteins for vitamin E and 4H-tamoxifen. The top 2 and 10% candidates of vitamin E binding proteins identified by TarFisDock respectively cover 30 and 50% of reported targets verified or implicated by experiments; and 30 and 50% of experimentally confirmed targets for 4H-tamoxifen appear amongst the top 2 and 5% of the TarFisDock predicted candidates, respectively. Therefore, TarFisDock may be a useful tool for target identification, mechanism study of old drugs and probes discovered from natural products. TarFisDock and PDTD are available at .

Ammonia (NH 3 ) can interact in the atmosphere with other trace chemical species, which can lead to detrimental environmental consequences, such as the formation of fine particulates and ultimately global climate change. China is a major agricultural country, and livestock numbers and nitrogen fertilizer use have increased drastically since 1978, following the rapid economic and industrial development experienced by the country. In this study, comprehensive NH 3 emissions inventories were compiled for China for 1980-2012. In a previous study, we parameterized emissions factors (EFs) considering ambient temperature, soil acidity, and the method and rate of fertilizer application. In this study, we refined these EFs by adding the effects of wind speed and new data from field experiments of NH 3 flux in cropland in northern China. We found that total NH 3 emissions in China increased from 5.9 to 11.1 Tg from 1980 to 1996, and then decreased to 9.7 Tg in 2012. The two major contributors were livestock manure and synthetic fertilizer application, which contributed 80-90 % of the total emissions. Emissions from livestock manure rose from 2.86 Tg (1980) to 6.16 Tg (2005, and then decreased to 5.0 Tg (2012); beef cattle were the largest source followed by laying hens and pigs. The remarkable downward trend in livestock emissions that occurred in 2007 was attributed to a decrease in the numbers of various livestock animals, including beef cattle, goats, and sheep. Meanwhile, emissions from synthetic fertilizer ranged from 2.

China has been experiencing fine particle (i.e., aerodynamic diameters ≤ 2.5 µm; PM2.5) pollution and acid rain in recent decades, which exert adverse impacts on human health and the ecosystem. Recently, ammonia (i.e., NH3) emission reduction has been proposed as a strategic option to mitigate haze pollution. However, atmospheric NH3 is also closely bound to nitrogen deposition and acid rain, and comprehensive impacts of NH3 emission control are still poorly understood in China. In this study, by integrating a chemical transport model with a high-resolution NH3 emission inventory, we find that NH3 emission abatement can mitigate PM2.5 pollution and nitrogen deposition but would worsen acid rain in China. Quantitatively, a 50% reduction in NH3 emissions achievable by improving agricultural management, along with a targeted emission reduction (15%) for sulfur dioxide and nitrogen oxides, can alleviate PM2.5 pollution by 11−17% primarily by suppressing ammonium nitrate formation. Meanwhile, nitrogen deposition is estimated to decrease by 34%, with the area exceeding the critical load shrinking from 17% to 9% of China’s terrestrial land. Nevertheless, this NH3 reduction would significantly aggravate precipitation acidification, with a decrease of as much as 1.0 unit in rainfall pH and a corresponding substantial increase in areas with heavy acid rain. An economic evaluation demonstrates that the worsened acid rain would partly offset the total economic benefit from improved air quality and less nitrogen deposition. After considering the costs of abatement options, we propose a region-specific strategy for multipollutant controls that will benefit human and ecosystem health.