CiteULike: neils's Jiang http://www.citeulike.org/user/neils/author/Jiang CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/2568656 <i>Nature (19 March 2008)</i> Kemp elimination catalysts by computational enzyme design Daniela Röthlisberger Olga Khersonsky Andrew Wollacott Lin Jiang Jason Dechancie Jamie Betker Jasmine Gallaher Eric Althoff Alexandre Zanghellini Orly Dym Shira Albeck Kendall Houk Dan Tawfik David Baker doi:10.1038/nature06879 Nature (19 March 2008) 2008-03-21T04:33:18-00:00 Nature 0028-0836 Nature Publishing Group catalysis computational design enzyme http://www.citeulike.org/user/neils/article/2709869 <i>Nature, Vol. 452, No. 7190. (24 April 2008), pp. 991-996.</i> The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) Ray Ming Shaobin Hou Yun Feng Qingyi Yu Alexandre Dionne-Laporte Jimmy Saw Pavel Senin Wei Wang Benjamin Ly Kanako Lewis Steven Salzberg Lu Feng Meghan Jones Rachel Skelton Jan Murray Cuixia Chen Wubin Qian Junguo Shen Peng Du Moriah Eustice Eric Tong Haibao Tang Eric Lyons Robert Paull Todd Michael Kerr Wall Danny Rice Henrik Albert Ming-Li Wang Yun Zhu Michael Schatz Niranjan Nagarajan Ricelle Acob Peizhu Guan Andrea Blas Ching Wai Christine Ackerman Yan Ren Chao Liu Jianmei Wang Jianping Wang Jong-Kuk Na Eugene Shakirov Brian Haas Jyothi Thimmapuram David Nelson Xiyin Wang John Bowers Andrea Gschwend Arthur Delcher Ratnesh Singh Jon Suzuki Savarni Tripathi Kabi Neupane Hairong Wei Beth Irikura Maya Paidi Ning Jiang Wenli Zhang Gernot Presting Aaron Windsor Rafael Navajas-Perez Manuel Torres Alex Feltus Brad Porter Yingjun Li Max Burroughs Ming-Cheng Luo Lei Liu David Christopher Stephen Mount Paul Moore Tak Sugimura Jiming Jiang Mary Schuler Vikki Friedman Thomas Mitchell-Olds Dorothy Shippen Claude Depamphilis Jeffrey Palmer Michael Freeling Andrew Paterson Dennis Gonsalves Lei Wang Maqsudul Alam doi:10.1038/nature06856 Nature, Vol. 452, No. 7190. (24 April 2008), pp. 991-996. 2008-04-23T19:37:29-00:00 Nature 452 7190 991 996 Nature Publishing Group genome genomics papaya plant sequence http://www.citeulike.org/user/neils/article/2439056 <i>BMC Bioinformatics, Vol. 9, No. 1. (2008)</i><br /><br />BACKGROUND:Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial.RESULTS:We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried.CONCLUSIONS:DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software on a Linux cluster platform. DOVIS: an implementation for high-throughput virtual screening using AutoDock Shuxing Zhang Kamal Kumar Xiaohui Jiang Anders Wallqvist Jaques Reifman doi:10.1186/1471-2105-9-126 BMC Bioinformatics, Vol. 9, No. 1. (2008) 2008-02-27T23:26:06-00:00 BMC Bioinformatics 9 1 autodock bioinformatics docking hpc screen software http://www.citeulike.org/user/neils/article/2319613 <i>Nat Methods, Vol. 5, No. 2. (February 2008), pp. 135-146.</i><br /><br />In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators. Protein production and purification. S Gräslund P Nordlund J Weigelt J Bray O Gileadi S Knapp U Oppermann C Arrowsmith R Hui J Ming S Dhe-Paganon HW Park A Savchenko A Yee A Edwards R Vincentelli C Cambillau R Kim SH Kim Z Rao Y Shi TC Terwilliger CY Kim LW Hung GS Waldo Y Peleg S Albeck T Unger O Dym J Prilusky JL Sussman RC Stevens SA Lesley IA Wilson A Joachimiak F Collart I Dementieva MI Donnelly WH Eschenfeldt Y Kim L Stols R Wu M Zhou SK Burley JS Emtage JM Sauder D Thompson K Bain J Luz T Gheyi F Zhang S Atwell SC Almo JB Bonanno A Fiser S Swaminathan FW Studier MR Chance A Sali TB Acton R Xiao L Zhao LC Ma JF Hunt L Tong K Cunningham M Inouye S Anderson H Janjua R Shastry CK Ho D Wang H Wang M Jiang GT Montelione DI Stuart RJ Owens S Daenke A Schütz U Heinemann S Yokoyama K Büssow KC Gunsalus doi:10.1038/nmeth.f.202 Nat Methods, Vol. 5, No. 2. (February 2008), pp. 135-146. 2008-02-01T14:36:35-00:00 Nat Methods 1548-7105 5 2 135 146 expression genomics proteins purification sg structure