A. Cámara-Artigas, J. Gavira, S. Casares, J. García‐Ruiz, F. Conejero-Lara, James P. Allen, Jose C. Martínez
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Pub Date : 2010-05-01DOI: 10.1107/S0907444910010073
M. Weiss
{"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}
Pub Date : 2009-09-01DOI: 10.1107/S0907444909018836
A. Scheidig
{"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}
Pub Date : 2007-12-04DOI: 10.1107/S0907444907058714
G. Murshudov, F. von Delft, C. Ballard
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 …
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Pub Date : 2007-06-01DOI: 10.1107/S0907444907013558
W. Hunter
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
首先，你应该对作者有所了解。理查德·迪克·迪克森(Richard Dick Dickerson)在剑桥做博士后时，参与了肌红蛋白的一些早期计算晶体学研究。当世界范围内大量可用的计算资源用于晶体学计算时，这是冒险的。成功的经验和现在对质子和蛋白质之间差异的了解使他走上了职业道路，在此期间，他研究了细胞色素蛋白的结构生物学及其分子进化，蛋白质与核酸的关联，以及可能与他最密切相关的工作，DNA结构的复杂性以及与药物的相互作用。因此，在为年轻读者建立了他的资历之后，让我们开始吧。迪克·迪克森认为1933年到1963年这段时间是结构分子生物学的起源。然后，他讲述了如何通过纤维衍射来研究蛋白质结构，并建立模型，然后如何对模型进行测试的故事。DNA是如何成为人们关注的焦点，又是如何成为制造这种大分子正确模型的竞赛的焦点。单晶衍射方法如何发展并最终揭示了肌红蛋白和血红蛋白的结构。然后，在经历了一段时间的巩固(干旱)之后，结构生物学领域开始腾飞。也许这听起来像是一本不错的小书，回顾了一个有趣的科学时期。它肯定不是。这是一本关于重要科学和塑造现代生物、化学和生物医学研究基石的真实人物的书。我们常常认为事情是理所当然的，尤其是在科学领域，因为进步似乎是无情的。有一种风险是，在我们获取事实的过程中，最初让我们获得事实的方法和推理、偶尔的意外发现和命运已经消失了。通常，在枯燥无味的科学出版物中，所有方面都被清楚地列出和解释，而缺少的是有时混乱的事实，即事情是如何以及为什么发生的。什么因素影响决策?所以，关于结构生物学的一些答案就在这里，迪克带我们踏上了一段旅程，从在利兹的阿斯特伯里工作，到伦敦的国王学院，再到剑桥，几次跨越大西洋。这个故事涉及到牛津的一张病床、大块大块的鲸鱼肉、在奥地利滑雪时组织的会议、猫头鹰眨眼的速度、纵火和邪恶的麦卡锡主义。这个故事涵盖了化学、物理和生物，并掺杂了一点政治和社会学。人类的力量是显而易见的，但也暴露了一些弱点;就像在生活的各个方面一样，这些可以决定成功或失败，也常常决定人们如何记住自己的贡献。作者对这个故事的许多贡献者的钦佩溢于言表。没有坏人，但有傲慢、无知的例子，至少有一个“可怕的自我”，谢天谢地，还有几个英雄，其中马克斯·佩鲁茨可能是最重要的(我想是我的偏见)。马克斯·佩鲁茨并没有得到所有的荣誉，鲍林、科里、沃森和克里克，当然还有布拉格都得到了这些荣誉。然后是分子本身，它们首先引起了这些天才的注意和想象。早期试图解决如何表示如此复杂的分子这一重要问题的尝试很有趣。早期模型的图像唤起了我对医学研究委员会分子生物学实验室的模型室的记忆，看到欧文·盖斯制作的美丽图像的复制是令人愉快的。不同的人可能会把重点放在其他地方，例如，我认为杰克萨姆纳的工作值得更多的细节(他被提到)，但迪克解释了包括什么，并证明了为什么。在某些情况下，这是一种非常私人的叙述，这是创造故事和玩家的积极因素。我喜欢融入一些原创文学的风格。把原稿和故事放在一起的策略效果很好。我在我的再版集里有一些这样的论文，连同早期关于溶菌酶的再版对我有很大的帮助，我毫不怀疑其他读者会觉得它们很有趣。不用数学也能清楚地解释衍射。这可能有助于一些读者理解这些重要的科学结果是如何得出的。对我来说，有一个地方行不通，那就是章节末尾的学习问题以及书末尾部分给出的答案。这本书可能是由于加州大学洛杉矶分校的课程而交付的，但它不太可能以完全相同的方式用于补充其他课程。然而，在这里发现的额外细节或轶事的结合，肯定会使最枯燥的讲座活跃起来。 我的建议是读这本书;这里有既吸引人又有教育意义的材料。谢谢你迪克。
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Pub Date : 2007-03-01DOI: 10.1107/S0907444906056113
P. Paufler
{"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}
Pub Date : 2006-10-01DOI: 10.1107/S0907444906035347
D. Stuart, E. Jones, K. Wilson, S. Daenke
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
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