Workshop on Methods for Macromolecular Modeling

描述（申请人提供）：计算方法越来越被认为是研究生物分子结构和功能的有价值的工具。模拟技术的进步，特别是在构象采样、快速静电学、分子动力学集成和量子力学计算等领域，对结构生物学产生了重大影响。新的算法方法、分层空间表示和改进的计算平台将继续增强大分子模拟的可靠性，并增加其在生物医学研究中的适用性和相关性。我们关于大分子建模M3方法的多学科研讨会是一系列国际会议中的第四次（1994年：堪萨斯州劳伦斯；1997年：德国柏林；2000年：纽约），其目的是将生物分子模拟计算工具的开发人员和那些利用（或有兴趣应用）计算机建模来解决大分子问题的生物和化学科学家聚集在一起。该研讨会将于2004年8月18日至21日在莱斯特大学举行，由SIAM（工业与应用数学学会）共同主办，作为SIAM生命科学新活动小组的一部分。正如前几次会议的成功所证明的那样——在参与者数量、实际成果、对年轻研究人员的影响以及对我们收集的卷的评论方面——我们的研讨会在研究进展和教育方面对社区产生了重要影响。这些会议的目标和主题与NIGMS生物信息学和计算生物学中心的许多活动以及NIH路线图主题/小组产生了很好的共鸣，包括结构生物学和跨学科研究（技术和方法的创新；消除结构障碍）。2004年重点关注的主题是：(1)力的评估、集成、优化和采样算法；(2)结构预测、反应路径、自由能分布和构象动力学方法；(3)力场表示和隐式溶剂；(4)量子/经典和经典弹性模型的多尺度技术；(5)酶催化、DNA建模和DNA/蛋白质系统的应用。该计划将为生物分子研究人员、计算机科学家和应用数学家之间的密切互动和科学交流提供及时和独特的机会。在我们的基因组革命时代及其推动的综合科学（例如，蛋白质组学，细胞组学和网络；代谢组学和生物技术），这种协同作用将激发新的想法，并帮助年轻科学家在计算科学和生物学的界面上进行跨学科研究。该计划将强调计算方法在医学相关问题中的应用，例如蛋白质折叠进展的后果和DNA聚合酶对疾病机制和新疗法的保真度。评估当前进展和确定该领域未来方向的工作将通过第一天的“焦点会议”完成，其中包括重要的介绍和小组讨论，并将据此编写一份报告。与之前的会议一样，我们希望收集受邀演讲者的文章，发表在b施普林格Verlag的《计算科学与工程（LNCSE）讲座笔记系列》中；该册将由组委会选定的成员编辑。除了精心设计的项目外，这些有形的记录有望通过教育跨学科界面的初级科学家，激发生物医学建模计算技术的新想法，并确定未来研究的关键领域，为社区和资助机构服务。此外，招募发言者和受支持的旅行者的目标是，通过积极鼓励这些参与者，为代表性不足的群体（妇女、少数民族和残疾科学家）获得良好的代表性。

DESCRIPTION (provided by applicant): Computational methods are increasingly being recognized as valuable tools for the study of biomolecular structure and function. Advances in simulation techniques, most notably in the areas of conformational sampling, fast electrostatics, molecular dynamics integration, and quantum-mechanical calculations, are having significant impact on structural biology. New algorithmic approaches, hierarchical spatial representations, and improved computing platforms will continue to enhance the reliability of macromolecular simulations and to increase their applicability and relevance to biomedical research. The purpose of our multidisciplinary workshop on Methods for Macromolecular Modeling M3--the fourth in a series of international meetings (1994: Lawrence, Kansas; 1997: Berlin, Germany; 2000: New York, NY)--is to bring together both developers of computational tools for biomolecular simulations and those biological and chemical scientists who utilize (or are interested in applying) computer modeling to macromolecular problems. The workshop will be held at the University of Leicester on August 18-21, 2004 and is co-sponsored by SIAM (Society for Industrial and Applied Mathematics), as part of SIAM's new Activity Group in the Life Sciences. As evidenced by the success of the prior meetings--in terms of participant number, tangible outcomes, influence on young researchers, and reviews of our collected volumes--our workshop has made important impact on the community in both research advances and education. These conference goals and themes resonate well with many activities at the NIGMS Center for Bioinformatics and Computational Biology as well as several additional NIH roadmap themes/groups, including structural biology and interdisciplinary research (innovations in technology and methods; removing structural barriers). The topics to be highlighted in 2004 are: (1) Algorithms for force evaluation, integration, optimization, and sampling; (2) Methods for structure prediction, reaction paths, free energy profiles, and conformational dynamics; (3) Representation of force fields and implicit solvent; (4) Multiscale techniques for quantum/classical and classical-elastic models; and (5) Applications to enzyme catalysis, DNA modeling, and DNA/protein systems. The program will provide a timely and unique opportunity for close interaction and scientific exchange among biomolecular researchers, computer scientists, and applied mathematicians. In our genomic revolution era and the integrative sciences it has propelled (e.g., proteomics, cellomics and networks; metabolomics, and biotechnology), such synergy will kindle new ideas and help prepare young scientists for crossdisciplinary research at the interface of computational science and biology. The program will emphasize the application of computational methods to problems of medical relevance, such as the consequences of protein folding advances and DNA polymerase fidelity to disease mechanisms and new therapeutics. The assessment of current progress and the identification of future directions in the field will be accomplished through a first day of "Focus Sessions," including key presentations and panel discussions, from which a report will be prepared. As in the prior meeting, we expect to collect articles by invited speakers for publication in Springer Verlag's Lecture Notes series in Computational Science & Engineering (LNCSE); the volume will be edited by selected members of the organizing committee. These tangible records, in addition to a carefully designed program, are expected to serve the community and the funding agencies by educating junior scientists at interdisciplinary interfaces, stimulating new ideas in computational techniques for biomedical modeling, and identifying key areas for future research. In addition, recruitment of speakers and supported travelers will be guided by the goal of obtaining a good representation for underrepresented groups (women, minorities, and scientists with disabilities) by proactively encouraging such participants.