Acta Crystallographica Section D: Biological Crystallography最新文献

{"title":"Understanding the polymorphic behaviour of a mutant of the alpha-spectrin SH3 domain by means of two 1.1 A structures","authors":"A. Cámara-Artigas, J. Gavira, S. Casares, J. García‐Ruiz, F. Conejero-Lara, James P. Allen, Jose C. Martínez","doi":"10.2210/PDB3M0Q/PDB","DOIUrl":"https://doi.org/10.2210/PDB3M0Q/PDB","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"28 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2011-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78468355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biomolecular Crystallography: Principles, Practice, and Applications to Structural Biology. By Bernhard Rupp. New York: Garland Science, Taylor and Francis Group, 2010. Pp. xxi + 809. Price (hardback) USD 145.00. ISBN 978‐0‐8153‐4081‐2.","authors":"M. Weiss","doi":"10.1107/S0907444910010073","DOIUrl":"https://doi.org/10.1107/S0907444910010073","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"49 1","pages":"640-641"},"PeriodicalIF":2.2,"publicationDate":"2010-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85044816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Experimental phasing and radiation damage","authors":"E. Garman, A. Pearson, C. Vonrhein","doi":"10.1107/S0907444910008796","DOIUrl":"https://doi.org/10.1107/S0907444910008796","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"103 1","pages":"0-0"},"PeriodicalIF":2.2,"publicationDate":"2010-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77085971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein Crystallography – A Concise Guide. By Eaton E. Lattman and Patrick J. Loll. Baltimore, Maryland, USA: John Hopkins University Press, 2008. Pp. 136. Price (hardback) US$ 70. ISBN 9780801888069.","authors":"A. Scheidig","doi":"10.1107/S0907444909018836","DOIUrl":"https://doi.org/10.1107/S0907444909018836","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"3 1","pages":"1011-1012"},"PeriodicalIF":2.2,"publicationDate":"2009-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86718234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Low-resolution structure determination and validation","authors":"R. Read, G. Kleywegt","doi":"10.1107/S0907444909000511","DOIUrl":"https://doi.org/10.1107/S0907444909000511","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"292 1","pages":"0-0"},"PeriodicalIF":2.2,"publicationDate":"2009-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90367606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular replacement","authors":"G. Murshudov, F. von Delft, C. Ballard","doi":"10.1107/S0907444907058714","DOIUrl":"https://doi.org/10.1107/S0907444907058714","url":null,"abstract":"The CCP4 Study Weekend 2007 was held at the University of Reading. Its focus was on the most widely used macromolecular crystallographic phasing technique, molecular replacement (MR). As the number of three-dimensional structures in the PDB increases dramatically so does the popularity and applicability of this technique. Therefore, it was timely to organize this popular gathering on this technique. The meeting was a mixture of descriptions of latest developments in popular and well known software (AMoRe, MOLREP, PHASER), new algorithms and challenging case studies. The topic of MR was previously visited at the 1992 and 2001 CCP4 Study Weekends, not surprisingly many old friends were welcomed back to bring the story up to date. The introductory session started by Phil Evans who outlined the ways and means of MR. He was followed by Stefano Trapatoni who described new algorithms on fast rotation functions implemented in the program AMoRe. Eleanor Dodson's lecture highlighted challenges of the technique and the importance of analysing the molecule under study even before starting to apply MR using bioinformatics techniques. Model generation and preparation are arguably the most important steps in increasing the odds of a good solution. In the model generation session Geoff Barton described various bioinformatics techniques for the sequence alignment that is at the heart of the MR technique. Andrey Lebedev described the built-in model generation techniques in MOLREP. Marc Delaure gave a talk on the use of normal mode analysis to generate a series of search models for molecular replacement. The final session of the first day was on validation of MR results and model completion. In this session talks by Gerard Bricogne, Serge Cohen and Paul Adams described how to validate the model and complete it using the packages BUSTER, ARP/wARP and PHENIX, respectively. The second day was on electron microscopy (EM) and MR, case studies and MR pipelines. In the first session Jorge Navaza gave a talk on the use of techniques developed in MR for EM, while Yong Xiong talked about the use of EM models as a search model for MR. Kevin Cowtan described various techniques for fitting the three-dimensional coordinates of a molecule into an electron-density map. In the session complicated cases Randy Read gave a talk on dealing with pseudo-translation, Michael Isupov and Adrian Lapthorn talked about challenging MR cases where the current MR software is not able to solve the structure automatically. They also described …","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"64 1","pages":"0 - 0"},"PeriodicalIF":2.2,"publicationDate":"2007-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0907444907058714","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61940361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Present at the Flood. By Richard E. Dickerson. Sunderland, Mass.: Sinauer Associates, Inc., 2005. Pp. 307. Price (paperback) US$ 36.95. ISBN 0-87893-168-6.","authors":"W. Hunter","doi":"10.1107/S0907444907013558","DOIUrl":"https://doi.org/10.1107/S0907444907013558","url":null,"abstract":"First you should know something of the author. Richard ‘Dick’ Dickerson was a participant in some of the early computational crystallography on myoglobin whilst a post-doc in Cambridge. This, when a significant amount of the world wide available computing resource was devoted to crystallographic calculations, was adventurous. The successful experience and now knowing the difference between protons and proteins set him on the career path during which he has investigated the structural biology of cytochrome proteins and their molecular evolution, protein–nucleic acid associations and perhaps the work with which he is most closely associated, the intricacies of DNA structure and interactions with drugs. So, with his credentials established for the younger readers, let us begin. Dick Dickerson identifies the period between 1933 and 1963 as the genesis of structural molecular biology. He then tells the story of how protein structure came to be investigated by fibre diffraction, and modelled and then how the models could be tested. How DNA came into the limelight and of the race to produce the correct model of this macromolecule. Of how single crystal diffraction methods progressed and eventually revealed the structures of myoglobin and hemoglobin. And then of how, following a period of consolidation (drought) the field of structural biology took off. Perhaps this sounds like a nice little book reviewing an interesting period in science. It most certainly is not. This is a book about important science and real people who shaped a cornerstone of modern biological, chemical and biomedical research. We often take things for granted especially in our science, as progress appears relentless. There is a risk that in our diet of facts the methods and reasoning, occasional serendipity and fate, that allowed to us obtain the facts in the first place are lost. Often, in the dryness of a scientific publication, where all aspects are clearly laid out and explained, what is missing is the sometimes chaotic reality of how and why things actually happened. What factors influenced decisions? So, with respect to structural biology some of the answers are to be found here as Dick takes us on a journey that evolves from Astbury working in Leeds, down to Kings College in London and up to Cambridge, and across the Atlantic a couple of times. The story involves a sickbed in Oxford, slabs of whale meat, conferences organised to coincide with good skiing in Austria, the speed of an owls blink, arson and sinister McCarthyism. The story encompasses chemistry, physics and biology with a little bit of politics and sociology mixed in. Human strengths are evident and some frailties are exposed; as in every aspect of life these can determine success or failure and often how contributions are remembered. The author’s admiration for the many of the contributors to the story shines through. There are no villains but there are examples of arrogance, ignorance, at least one ‘monstrous eg","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"139 1","pages":"750-750"},"PeriodicalIF":2.2,"publicationDate":"2007-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77464056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PET Chemistry. The Driving Force in Molecular Imaging. Edited by P. A. Schubiger, L. Lehmann & M. Friebe. Pp. xii + 339. Berlin: Springer-Verlag, 2007. Price (hardback) Euro 88.76. ISBN-103-540-32623-5.","authors":"P. Paufler","doi":"10.1107/S0907444906056113","DOIUrl":"https://doi.org/10.1107/S0907444906056113","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"230 1","pages":"420-420"},"PeriodicalIF":2.2,"publicationDate":"2007-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79696275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SPINE: Structural Proteomics in Europe - The best of both worlds","authors":"D. Stuart, E. Jones, K. Wilson, S. Daenke","doi":"10.1107/S0907444906035347","DOIUrl":"https://doi.org/10.1107/S0907444906035347","url":null,"abstract":"Division of Structural Biology, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, England, and York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, England The concept of structural genomics arose in the mid to late 1990s in the USA and Japan as a response to the success of high-throughput (HTP) sequencing methods applied to whole genomes (see http://www.isgo.org). It was imagined that similar HTP methods could be applied to obtain three-dimensional structures of all the proteins (the ‘proteome’) of an organism, which would in particular be an efficient way of filling in the gaps in observed ‘fold-space’. This vision led to the investment of substantial sums of money into large-scale structural genomics projects in the USA [e.g. nine projects funded by the NIH/NIGMS Protein Structure Initiative (PSI) from September 2000 to June 2005, http://www.nigms.nih.gov/psi/] and Japan (e.g. the massive RIKEN project, http:// www.rsgi.riken.go.jp/). These were characterized by the concentration of resources into a small number of large centres, the development of novel, automated technologies to permit a HTP pipeline approach to structure determination, and a focus on novel folds as the major target criteria. The US-based projects, in addition, required immediate public deposition of structural data whereas the Japanese RIKEN project also aimed to support Japanese industry, precluding deposition in advance of patent evaluation. Europe was slower in implementing HTP approaches to structural biology. The Protein Structure Factory in Berlin, Germany (http://www.proteinstrukturfabrik.de/) led the way, followed by the Oxford Protein Production Facility (OPPF) in Oxford, UK (http:// www.oppf.ox.ac.uk/) and the Genopoles in France (notably Gif, Marseille and Strasbourg, http://rng.cnrg.fr/). However, it was not until October 2002 that the first Europe-wide project began. This was a three-year project funded by the EU FP5 programme called SPINE: Structural Proteomics IN Europe (http://www.spineurope.org). SPINE, a ‘second generation’ structural genomics project (indeed purposefully called a Structural Proteomics project to draw a distinction), made some radical departures from the firstgeneration initiatives, while at the same time obviously benefiting from the experience and technology development of the preceding projects. The challenge set for SPINE was to push forward with cutting-edge technologies aimed at biomedically relevant targets at the same time as generating a pan-European integration on biomedically focused structural proteomics. The SPINE consortium comprised","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"31 1","pages":"0-0"},"PeriodicalIF":2.2,"publicationDate":"2006-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91017200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Get-Phases Beijing 2005","authors":"Xiaodan Su, T. Terwilliger","doi":"10.1107/S0907444906024759","DOIUrl":"https://doi.org/10.1107/S0907444906024759","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"36 1","pages":"945-945"},"PeriodicalIF":2.2,"publicationDate":"2006-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76928217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}