Seventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction
2007; Wiley; Volume: 69; Issue: S8 Linguagem: Inglês
10.1002/prot.21849
ISSN1097-0134
AutoresTina L. Trapane, Eaton E. Lattman,
Tópico(s)Genetics, Bioinformatics, and Biomedical Research
ResumoOver the past 12 years, the CASP experiment has provided a community-wide forum for the testing and comparison of structure prediction methods. It operates by soliciting from interested groups, structure predictions of target molecules whose structures are (or will be) known, but have not yet been made public during the time of prediction and assessment. The Seventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, more colloquially known as CASP7, was held at the Asilomar Conference Center in Pacific Grove, California, 26–30 November, 2006. As usual, the meeting generated high levels of interest and enthusiasm. A total of 253 unique research groups participated in the experiment, including 98 prediction servers. Through the generosity of structural research groups, 104 prediction targets (including 124 domains) were made available for predictors. In addition, “best models” from seven previous CASP5 and CASP6 targets were offered as challenges for further refinements. All together, these factors show an intense commitment on the part of those in the field to the structure prediction enterprise. Since 1995, Proteins has provided a forum, as a supplement to its regular print issues, for each of the six previous CASP experiments. We are collectively proud of the part the journal has played in bringing hard data regarding structure prediction into the literature. John Moult, CARB, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Tim Hubbard, Wellcome Trust Sanger Institute, Hinxton, UK Andriy Kryshtafovych, University of California, Davis, USA Burkhard Rost, CUBIC, Columbia University, USA, and Anna Tramontano, University of Rome “La Sapienza”, Italy Anna Tramontano and John Moult also contributed extensively to this issue of Proteins, which contains commentary, assessment, and results arising from CASP7. They have played, along with Tim Hubbard and Burkhard Rost, the major editorial roles to ensure that all articles published herein have received the necessary vetting and peer review. Over the years, these four have worked with enormous energy and dedication to bring the scientific aspects of these CASP issues together. The Joint Center for Structural Genomics (JCSG), University of California, San Diego, CA The Northeast Structural Genomics Consortium (NESG), Rutgers University, Piscataway, NJ The Structural Genomics Consortium (SGC), University of Oxford, Oxford, UK The Midwest Center for Structural Genomics (MCSG), Argonne National Laboratory, Argonne, IL, and The Center for Eukaryotic Structural Genomics (CESG), University of Wisconsin-Madison, WI Structural genomics centers located in the United States are involved in the Protein Structure Initiative, which is sponsored by the National Institute of General Medical Sciences at NIH. The purpose of the initiative is to map protein structure space by determining a set of landmark protein structures—in all probability, several thousand. The idea is that most newly discovered proteins will be within modeling distance of a landmark structure. The homology modeling category in CASP is obviously of great practical importance here. This has not, unfortunately, been an area where dramatic progress has been made. However, even incremental improvements that increase the “modeling distance” are of great value. Torsten Schwede, University of Basel, Switzerland (template-based modeling) Neil Clarke, Genome Institute of Singapore (template-free modeling) Randy Read, University of Cambridge, UK (high resolution modeling), and Alfonso Valencia, National Centre for Biotechnology, Madrid (function prediction) These principal assessors—whose task is thankless, albeit essential—were assisted by the following colleagues: Gayatri Chavali, Jürgen Kopp, Lorenza Bordoli, James Battey, Florian Kiefer, Ralf Jauch, Hock Chuan Yeo, Prasanna R. Kolatkar, Gonzalo López, Ana Rojas, and Michael Tress. In addition to the above, many others contributed to CASP7. The Protein Structure Prediction Center at the Genome Center, University of California, Davis, served as the indispensable nexus for data management and security for the CASP experiment. The Center is supported by the National Institutes of Health and the US National Library of Medicine. Meeting support was provided from the NIH Institute of General Medical Sciences, by the BioSapiens Network of Excellence (funded by the European Commission FP6 Programme), and by Hewlett Packard. Without the generous patronage of these contributors, the CASP7 experiment as reported here could not have come about. We are grateful to Ms. Stefanie Alaimo, Assistant Managing Editor for Proteins, at John Wiley & Sons for support in manuscript handling. Above all, we send a million thanks and a round of applause to Dr. Anna Tramontano for her efforts in bringing this issue together. Over the years we have taken great pride in bringing the forefront of the protein structure prediction field to the community at large. It is our continued pleasure to offer to the Proteins readership this body of information on the most recent CASP efforts. Tina L. Trapane*, Eaton E. Lattman , * Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, Department of Biophysics, The Johns Hopkins University, Baltimore, Maryland 21218.
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