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Section I. Protein Target Selection, Bioinformatic Approaches, and Data Management 1 Target Selection for Structural Genomics: An Overview ................ 3 Russell L. Marsden and Christine A. Orengo 2 A General Target Selection Method for Crystallographic Proteomics .................................... ....... 27 Gautier Robin, Nathan P. Cowieson, Gregor Guncar Jade K. Forwood, Pawel Listwan, David A. Hume, Bostjan Kobe, Jennifer L. Martin, and Thomas Huber 3 Target Selection: Triage in the Structural Genomics Battlefield...... 37 James Raftery 4 Data Management in Structural Genomics: An Overview ............ 49 Sabrina Haquin, Eric Oeuillet, Anne Pajon, Mark Harris, Alwyn T Jones, Herman van Tilbeurgh, John L. Markley, Zolt Zolnai, and Anne Poupon 5 Data Deposition and Annotation at the Worldwide Protein Data Bank........................................ ........................... 81 Shuchismita Dutta, Kyle Burkhardt, Ganesh J. Swaminathan, Takashi Kosada, Kim Henrick, Haruki Nakamura, and Helen M. Berman 6 Prediction of Protein Disorder............................... 103 Zsuzsanna Dosztdnyi and Peter Tompa 7 Protein Dom ain Prediction ............................................................ 117 Helgi Ingolfsson and Golan Yona 8 Protein Structure Modeling with MODELLER ............................ 145 Narayanan Eswar, David Eramian, Ben Webb, Min-Yi Shen, and Andrej Sali Section II. Protein Production 9 High Throughput Cloning with Restriction Enzymes ................... 163 Volker Sievert, Asgar Ergin, and Konrad Biissow 10 Automated Recombinant Protein Expression Screening in Escherichia coli ..................................... 175 Didier Busso, Matthieu Stierld, Jean-Claude Thierry, and Dino Moras 11 From No Expression to High-Level Soluble Expression in Escherichia coli by Screening a Library of the Target Proteins with Randomized N-Termini ....................................... . 187 Kyoung Hoon Kim, Jin Kuk Yang, Geoffrey S. Waldo, Thomas C. Terwilliger and Se Won Suh 12 Application of High-Throughput Methodologies to the Expression of Recombinant Proteins in E. coli................... 197 Yoav Peleg and Tamar Unger 13 A High Throughput Platform for Eukaryotic Genes ..................... 209 Yunjia Chen, Shihong Qiu, Chi-Hao Luan, and Ming Luo 14 High Throughput Production of Recombinant Human Proteins for Crystallography......................... 221 Opher Gileadi, Nicola A. Burgess-Brown, Steve M. Colebrook, Georgina Berridge, Pavel Savitsky, Carol E. A. Smee, Peter Loppnau, Catrine Johansson, Eidarus Salah, and Nadia H. Pantic 15 Assembly of Protein Complexes by Coexpression in Prokaryotic and Eukaryotic Hosts: an Overview ...................... 247 Anastassis Perrakis and Christophe Romier 16 Cell-Free Protein Synthesis for Analysis by NMR Spectroscopy............................. 257 Margit A. Apponyi, Kiyoshi Ozawa, Nicholas E. Dixon, and Gottfried Otting 17 A Medium or High Throughput Protein Refolding Assay ............ 269 Nathan P Cowieson, Beth Wensley, Gautier Robin, Gregor Guncar Jade Forwood, David A. Hume, Bostjan Kobe, and Jennifer L. Martin 18 Structural Proteomics of Membrane Proteins: a Survey of Published Techniques and Design of a Rational High Throughput Strategy ........................................ 277 Melissa Swope Willis and Christopher M. Koth Section III. Biophysical and Functional Characterization of Proteins 19 Methods for Protein Characterization by Mass Spectrometry, Thermal Shift (ThermoFluor) Assay, and Multiangle or Static Light Scattering ................................ ............................ 299 Joanne E. Nettleship, James Brown, Matthew R. Groves, and Arie Geerlof 20 High Throughput Methods for Analyzing Transition Metals in Proteins on a Microgram Scale ..................................... 319 Anelia Atanassova, Martin H6gbom, and Deborah B. Zamble 21 High Throughput Screening of Purified Proteins for Enzymatic Activity................................ 331 Michael Proudfoot, Ekaterina Kuznetsova, Stephen A. Sanders, Claudio E Gonzalez, Greg Brown, Aled M. Edwards, Cheryl H. Arrowsmith, and Alexander E Yakunin Section IV. Structural Characterization of Proteins 22 Strategies for Improving Crystallization Success Rates ................ 345 Rebecca Page 23 Protein Crystallization in Restricted Geometry: Advancing Old Ideas for Modern Times in Structural Proteomics ........................................ 363 Joseph D. Ng, Raymond C. Stevens, and Peter Kuhn 24 Fluorescence Approaches to Growing Macromolecule Crystals ..... 377 Marc Pusey, Elizabeth Forsythe, and Aniruddha Achari 25 Efficient Macromolecular Crystallization Using Microfluidics and Randomized Design of Screening Reagents....... 387 Andrew P May and Brent W Segelke 26 Increasing Protein Crystallization Screening Success with Heterogeneous Nucleating Agents .................... .................... 403 Anil S. Thakur, Janet Newman, Jennifer L. Martin, and Bostjan Kobe 27 High Throughput pH Optimization of Protein Crystallization......... 411 Ran Meged, Orly Dym, and Joel L. Sussman 28 Automated Structure Solution with the PHENIX Suite ................ 419 Peter H. Zwart, Pavel V Afonine, Ralf W Grosse-Kunstleve, Li-Wei Hung, Thomas R. loerger Airlie J. McCoy, Erik McKee, Nigel W Moriarty, Randy J. Read, James C. Sacchettini, Nicholas K. Sauter, Laurent C. Storoni, Thomas C. Terwilliger, and Paul D. Adams 29 NMR Screening for Rapid Protein Characterization in Structural Proteomics ........................................... 437 Justine M. Hill 30 Microcoil NMR Spectroscopy: a Novel Tool for Biological High Throughput NMR Spectroscopy ......................... 447 Russell E. Hopson and Wolfgang Peti 31 Protein Structure Determination Using a Combination of Cross-Linking, Mass Spectrometry, and Molecular Modeling .... 459 Dmitri Mouradov, Gordon King, Ian L. Ross, Jade K. Forwood, David A. Hume, Andrea Sinz, Jennifer L. Martin, Bostjan Kobe, and Thomas Huber Section V. Structural Proteomics Initiatives Overviews 32 Structural Genomics of Minimal Organisms: Pipeline and Results ....................................... 477 Sung-Hou Kim, Dong-Hae Shin, Rosalind Kim, Paul Adams, and John-Marc Chandonia 33 Structural Genomics of Pathogenic Protozoa: an Overview ......... 497 Erkang Fan, David Baker Stanley Fields, Michael H. Gelb, Frederick S. Buckner Wesley C. Van Voorhis, Eric Phizicky, Mark Dumont, Christopher Mehlin, Elizabeth Grayhack, Mark Sullivan, Christophe Verlinde, George DeTitta, Deirdre R. Meldrum, Ethan A. Merritt, Thomas Earnest, Michael Soltis, Frank Zucker, Peter J. Myler Lori Schoenfeld, David Kim, Liz Worthey, Doug LaCount, Marissa Vignali, Jizhen Li, Somnath Mondal, Archna Massey, Brian Carroll, Stacey Guide, Joseph Luft, Larry DeSoto, Mark Holl, Jonathan Caruthers, Jiirgen Bosch, Mark Robien, Tracy Arakaki, Margaret Holmes, Isolde Le Trong, and Wim G. J. Hol 34 High Throughput Crystallography at SGC Toronto: an Overview ........................................ 515 Alexey Bochkarev and Wolfram Tempel 35 The Structural Biology and Genomics Platform in Strasbourg: an Overview ..................................... 523 Didier Busso, Jean-Claude Thierry, and Dino Moras 36 Bacterial Structural Genomics Initiative: Overview of Methods and Technologies Applied to the Process of Structure Determination ............................ 537 Miroslaw Cygler, Ming-ni Hung, John Wagner, and Allan Matte 37 High Throughput Protein Production and Crystallization at NYSGXRC ..................................... 561 Michael J. Sauder; Marc E. Rutter, Kevin Bain, Isabelle Rooney, Tarun Gheyi, Shane Atwell, Devon A. Thompson, Spencer Emtage, and Stephen K. Burley 38 Overview of the Pipeline for Structural and Functional Characterization of Macrophage Proteins at the University of Queensland ........................................ 577 Weining Meng, Jade K. Forwood, Gregor Guncar Gautier Robin, Nathan P. Cowieson, Pawel Listwan, Dmitri Mouradov, Gordon King, lan L. Ross, Jodie Robinson, Munish Puri, Justine M. Hill, Stuart Kellie, Thomas Huber, David A. Hume, Jennifer L. Martin, and Bostjan Kobe 39 Structural Genomics of the Bacterial Mobile Metagenome: an Overview ......................................... 589 Andrew Robinson, Amy P Guilfoyle, Visaahini Sureshan, Michael Howell, Stephen J. Harrop, Yan Boucher, Hatch W Stokes, Paul M. G. Curmi, and Bridget C. Mabbutt