Pingping Zhang, Zhonghu He,Yan Zhang, Xianchun Xia, Dongshen Chen, and Yong Zhang

S.R. Upadhyay ; K.B. Koirala ; D.C. Paudel ; S.N. Sah ; D. Sharma ; D.B. Gurung ; R.C. Prasad ; R.B. Katuwal ; B.B. Pokhrel ; R.K. Mahato ; R. Dhakal ; N.B. Dhami ; T.P. Tiwari ; G. Ortiz- Ferrara ; R.C. Sharma

Among the many progresses in Marine Aquaria hobby in the recent years, the use of protein skimmers was, by far, one of the greatest milestones in maintaining salt water aquarium animals. Organic compounds, being bipolar in nature, provide an opportunity for waste extraction via injection of air into the skimmer body which served the dual function of extraction of these compounds while aerating the water. Since their inception, there has been much advancement in the design and functionality of Protein Skimming.

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.