分子与量子计算机前瞻

概述了蛋白质计算机和ＤＮＡ计算机等生物分子计算机以及量子计算机研究领域的新进展。     

中药补气与活血分子作用机理的计算机模拟

采用分子相似性分析、分子对接和生物网络技术等计算机模拟方法对治疗冠心病的中药活血与补气的分子作用机理进行研究. 结果表明, 计算机模拟方法可以体现化合物的结构差异, 并提示中药中化学成分与相关靶标相互作用的分子机理, 而生物网络的构建和分析可以将化学成分的聚类、差异, 以及有效成分与相关靶标的复杂分子作用机理可视化.     

生物分子计算进展*

由于生物分子在化学反应中具有高度的并行性和识别能力,使生物分子计算在解决组合优化问题中显示出巨大的优势。生物分子计算已成功地应用于计算哈密顿路径、最大集合以及逻辑运算中的SAT类问题等NP完全问题。本文总结了生物分子计算的基本思想与计算方法、生物分子计算的应用与进展,并对生物分子计算的发展趋势作了评述。     

计算机辅助糖苷酶分子设计与改造研究进展

糖苷酶作为一种重要的生物催化剂,在工业生物催化领域有着广阔的应用前景。但天然糖苷酶存在催化活性低、热稳定性和底物选择性差等缺点,严重限制了它在规模化生产中的推广应用。近年,有关糖苷酶催化机制与结构功能关系的研究备受关注,特别是计算机辅助酶设计在相关研究领域发挥着越来越重要的作用。本文综述了糖苷酶分子设计改造过程中应用的计算机辅助方法：包括同源比对、分子对接以及动力学模拟;系统阐述了这些计算方法在糖苷酶的结构与功能关系解析、酶催化分子机制、酶催化性能改造方面的应用现状。通过对上述方法的深入分析可以预见,计算机辅助方法将成为糖苷酶分子设计改造的重要手段,并且开发智能精准的计算分析方法将成为加快酶分子定向改造的新发展趋势。     

DNA分子器件*

DNA不仅是一种重要的生物遗传物质,而且可以在生命科学以外的领域,尤其是在信息科学、材料科学中发挥重要作用.作为重要的部件,DNA分子器件的研究引起了科学家们的注意.本文对DNA分子器件的发展以及DNA分子器件的实现和应用前景及不足进行了较详尽的评述.     

药物分子设计和核酸的分子识别分析

分子识别分析理论应用于药物分子设计是新药开发的要求，也是分析化学一个极具潜力的发展方向，分子识别分析不仅为药物分子设计提供了生物大分子的组成，结构基基本信息，还为了解药物分子与生物大分子相互作用位点及作用方式提供了模型，本文评述了与药物分子设计中有关的核酸物质的分子识别分析，它们是设计好的抗癌药物的基础。     

生物纳米孔分析技术研究进展

生物纳米孔传感技术因其快速、低成本、无需荧光标记等优点,在化学和生物等诸多研究领域得到广泛应用,已发展成为一种新颖的、独具特色的单分子分析手段。该技术目前主要应用于DNA测序研究,同时在单分子分析领域也取得了令人瞩目的成就。该文简要介绍了生物纳米孔分析技术的原理和生物孔的种类,主要总结了近20年来生物纳米孔在DNA测序和单分子分析中的研究进展并予以了展望。     

DNA计算机

DNA 计算机是一种基于DNA 生化反应, 与传统计算机完全不同的新型生物计算机。本文对DNA 计算的原理、实现、发展以及实现DNA 计算机的可行性、优势与不足进行了较详尽的评述。     

DNA分子构成及其分析测定方法

ＤＮＡ是生物体主要的遗传物质,有关ＤＮＡ的研究是揭示生物遗传奥秘的基础。在对ＤＮＡ的分子构型－双螺旋结构及ＮＤＡ分子组成分析的基础上,探讨了ＤＮＡ的某些性质,论述了ＤＮＡ分析测定方法的发展过程,介绍了近几年来国际国内对ＤＮＡ分析测定的新成果及发展方向。     

生物分子功能化碳纳米管

利用生物分子功能化碳纳米管,使其具备生物相容性和特殊的识别功能并引入生物体系是一项极具应用潜力的研究.如何利用不同种类的生物分子功能化碳纳米管则是该领域须解决的一个关键问题.本文综述了利用生物分子酶、蛋白质、氨基酸、肽螺旋、DNA功能化碳纳米管的最新研究进展,重点介绍了碳纳米管侧壁与端口的DNA功能化以及碳纳米管的DNA填充,并对DNA功能化碳纳米管在生物传感器、电化学检测及DNA操纵碳纳米管自组装方面的应用作了阐述.     

计算机分子模拟在分子印迹技术中的应用

传统的分子印迹技术对模板分子、功能单体、交联剂、致孔剂等的筛选往往依靠经验,常通过反复实验对合成条件进行优化,存在实验周期长、耗材量大等问题。计算机分子模拟技术的应用在实验过程中起到可预见性指导作用,可以实现精准识别位点的裁制、识别驱动力的设计,通过结合能等物化特征参数计算优化识别体系的稳定性,从而合理选择模板分子、功能单体、交联剂、致孔剂,优化聚合条件,以提高聚合物识别特异性和亲和力,缩短实验周期,更符合绿色化学的理念。本文简单介绍了计算机分子模拟技术,重点对其在分子印迹技术中的指导作用进行了综述,并对其在分子印迹技术中的应用进行了展望。     

计算机化学模拟—分子构象识别的新方法

简介了几种利用计算机图形技术研究化合物分子构象的新方法。重点介绍了分子力学计算方法中的系统搜索、随机搜索方法和分子动力学计算方法中的模拟淬火、模拟退火等新技术 ,为药物分子设计中受体与配体分子构象的识别提供了合理可行的方法。     

Connectable DNA Logic Gates: OR and XOR Logics

Modern computer processors are based on semiconductor logic gates connected to each other in complex circuits. This study contributes to the development of a new class of connectable logic gates made of DNA in which the transfer of oligonucleotide fragments as input/output signals occurs upon hybridization of DNA sequences. The DNA strands responsible for a logic function form associates containing immobile DNA four‐way junction structures when the signal is high and dissociate into separate strands when the signal is low. A basic set of logic gates (NOT, AND, and OR) was designed. Two NOT gates, two AND gates, and an OR gate were connected in a network that corresponds to an XOR logic function. The design of the logic gates presented here may contribute to the development of the first biocompatible molecular computer.     

Anion Sensors as Logic Gates: A Close Encounter?

Computers have become smarter, smaller, and more efficient due to the downscaling of silicon‐based components. Top‐down miniaturisation of silicon‐based computer components is fast reaching its limitations because of physical constraints and economical non‐feasibility. Therefore, the possibility of a bottom‐up approach that uses molecules to build nano‐sized devices has been initiated. As a result, molecular logic gates based on chemical inputs and measurable optical outputs have captured significant attention very recently. In addition, it would be interesting if such molecular logic gates could be developed by making use of ion sensors, which can give significantly sensitive output information. This review provides a brief introduction to anion receptors, molecular logic gates, a comprehensive review on describing recent advances and progress on development of ion receptors for molecular logic gates, and a brief idea about the application of molecular logic gates.     

Dynamics of solvation of an ion in a dense dipolar liquid

A molecular theory of the dynamics of solvation of an ion in a dense dipolar liquid is presented. The theory is based on an extended hydrodynamic approach that properly includes the interparticle correlations that are present at molecular length scales. The effects of the solvent inertial and viscoelastic responses are also included consistently. Numerical studies reveal rich relaxation behaviour such as short-time oscillations followed by a slow long-time decay. The results are in semi-quantitative agreement with recent computer simulation studies.     

Biomolecular modeling: Goals, problems, perspectives

Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling.     

Visualizing The Future of Molecular Graphics

Abstract

The field of computer graphics has played an important role in the advancement of structural molecular biology and in the development of structure-based drug design. This article will provide a brief background on the development of this technology, and then focus on the current trends and future directions in molecular graphics and how they will impact the practice of molecular modeling and design. Specific areas that will be covered include: 1) the development of surface and volume based representations of molecular properties and interactions; 2) new approaches to modeling flexible and multi-component structures, and 3) the impact of object-oriented graphics-based programming and the rapidly growing use of network based computing.     

EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases

The completion of the Human Genome Project, the growing effort on proteomics, and the Structural Genomics Initiative have recently intensified the attention being paid to reliable computer docking programs able to identify molecules that can affect the function of a macromolecule through molecular complexation. We report herein an automated computer docking program, EUDOC, for prediction of ligand-receptor complexes from 3D receptor structures, including metalloproteins, and for identification of a subset enriched in drug leads from chemical databases. This program was evaluated from the standpoints of force field and sampling issues using 154 experimentally determined ligand-receptor complexes and four "real-life" applications of the EUDOC program. The results provide evidence for the reliability and accuracy of the EUDOC program. In addition, key principles underlying molecular recognition, and the effects of structural water molecules in the active site and different atomic charge models on docking results are discussed. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1750-1771, 2001