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51. 发明申请

US20030176992A1 Visualization method of RNA pseudoknot structures 有权
标题翻译： RNA pseudoknot结构的可视化方法
公开(公告)号：US20030176992A1
公开(公告)日：2003-09-18
申请号：US10170251
申请日：2002-06-11
发明人： Kyung sook Han , Woo taek Kim , Yujin Lee , Hong-Jin Kim
IPC分类号： C12Q001/68 , G06G007/48 , G06G007/58 , G06F019/00 , G01N033/48 , G01N033/50
CPC分类号： G06F19/26 , G06F19/16 , Y10S707/99943
摘要： Disclosed is a visualization method of RNA pseudoknot structures. The method of the invention comprises the steps of setting criteria required for visualizing RNA pseudoknots, setting structural elements and data structures for representing a whole RNA structure containing pseudoknots, determining an input format for visualization and a drawing order of the structure, determining connectivity relations between regular loops and stems in the structure and between pseudoknot loops and stems in the structure, calculating radii of the regular loop and the PK loop, calculating coordinates of bases in the regular loops, setting internal angles of the PK loops, calculating startAngles of the regular loops and angles of the stem, determining positions of the pseudoknots in the PK loops, and drawing the pseudoknots and the whole RNA structure containing the pseudoknots.
摘要翻译：披露了RNA伪鸟结构的可视化方法。本发明的方法包括以下步骤：设置可视化RNA伪鸟所需的标准，设定用于表示含有假鸟的整个RNA结构的结构元件和数据结构，确定可视化的输入格式和结构的绘制顺序，确定结构元件之间的连接关系结构中的规则环和茎，结构中的假核心和茎之间，计算常规循环和PK循环的半径，计算常规循环中基数的坐标，设置PK循环的内部角度，计算正常循环的起始角度茎的环和角度，确定PK环中假鸟的位置，以及绘制含有假鸟的假核和整个RNA结构。

52. 发明申请

US20030176662A1 Structure-based hepatitis c virus drug design 有权
标题翻译：基于结构的丙型肝炎病毒药物设计
公开(公告)号：US20030176662A1
公开(公告)日：2003-09-18
申请号：US10312490
申请日：2003-04-22
发明人： Martino Bolognesi , Guido Grandi
IPC分类号： G06G007/48 , G06G007/58 , A61K039/395 , C07K016/28
CPC分类号： G01N33/6893 , C07K14/70596 , C07K2299/00 , G01N33/5767 , G16B15/00
摘要： The extracellular loop of CD81 is a cellular receptor for the E2 protein of hepatitis C virus. A CD81 crystal structure has been elucidated and is provided for use in the structure-based design of compounds which bind to CD81 and thus block the binding of HCV. Methods such as docking and de novodrug design can be used.
摘要翻译： CD81的细胞外环是丙型肝炎病毒E2蛋白的细胞受体。已经阐明了CD81晶体结构，并且被提供用于结合CD81的化合物的基于结构的设计，从而阻断HCV的结合。可以使用诸如对接和novodrug设计的方法。

53. 发明申请

US20030148386A1 Method for drug design using comparative molecular field analysis (CoMFA) extended for multi-mode/multi-species ligand binding and disposition 审中-公开
标题翻译：使用比较分子场分析（CoMFA）扩展用于多模式/多物种配体结合和处置的药物设计方法
公开(公告)号：US20030148386A1
公开(公告)日：2003-08-07
申请号：US10292800
申请日：2002-11-12
申请人： North Dakota State University
发明人： Stefan Balaz , Viera Lukacova
IPC分类号： G01N033/53 , G06G007/48 , G06G007/58 , G06F019/00 , G01N033/48 , G01N033/50
CPC分类号： G16B15/00 , G16B40/00 , G16C99/00
摘要： An advance in the art of comparative molecular field analysis allows the evaluation of multiple binding modes for the interactions of single or multiple species of ligand molecules with a common macromolecule.
摘要翻译：比较分子场分析技术的进步允许评估多种结合模式用于单一或多种配体分子与普通大分子的相互作用。

54. 发明申请

US20030144823A1 Scale-free network inference methods 审中-公开
标题翻译：无量纲网络推理方法
公开(公告)号：US20030144823A1
公开(公告)日：2003-07-31
申请号：US10286372
申请日：2002-11-01
发明人： Jeffrey J. Fox , Colin Hill , Vipul Periwal
IPC分类号： G06G007/48 , G06G007/58
CPC分类号： G01N33/5091 , G01N2333/4739 , G16B5/00
摘要： Presently disclosed are methods for inferring a network model of the interactions of biological molecules and systems for practicing such methods. The systems and methods described herein provide a systematic and computationally feasible solution to the problem of rational inference of the architecture of biological networks, based on a combination of rational and statistical evaluations of quantitative and qualitative data. These methods constrain the search space of possible networks and, in some embodiments, allow the online addition of new data into an existing model without any interruption in analysis. Additionally, these methods can provide a quantitative evaluation of the confidence levels associated with the putative network architectures discovered thereby. The methods naturally incorporate latent nodes in the search space of possible architectures; hence, the system is also capable of predicting new interactions and/or substrates for the biological systems being studied.
摘要翻译：目前公开的是用于推断生物分子和系统的相互作用的网络模型用于实施这种方法的方法。基于对定量和定性数据的理性和统计学评估的组合，本文所述的系统和方法为生物网络结构的合理推理问题提供了系统和计算上可行的解决方案。这些方法限制了可能网络的搜索空间，并且在一些实施例中允许将新数据在线添加到现有模型中而不会有任何中断的分析。此外，这些方法可以提供与由此发现的推定网络架构相关联的置信水平的定量评估。这些方法自然地将可能的架构的潜在节点并入搜索空间; 因此，该系统还能够预测正在研究的生物系统的新的相互作用和/或底物。

55. 发明申请

US20030144472A1 Method of identifying designable protein backbone configurations 审中-公开
标题翻译：鉴定可设计蛋白质主链构型的方法
公开(公告)号：US20030144472A1
公开(公告)日：2003-07-31
申请号：US10066496
申请日：2002-01-31
申请人： NEC Research Institute, Inc.
发明人： Eldon Emberly , Chao Tang , Ned S. Wingreen
IPC分类号： C07K014/00 , C07K007/08 , G06G007/48 , G06G007/58
CPC分类号： C07K1/00 , C07K14/00 , C07K14/001
摘要： The invention provides a method for identifying new designable protein backbone configurations. The method includes the steps of: (a) specifying a fixed number of secondary structural elements having a set of dihedral angle pairs (b) generating a set of stacks comprising said secondary structural elements; and (c) evaluating designability of said stacks.
摘要翻译：本发明提供了一种用于鉴定新的可设计蛋白质主链构型的方法。该方法包括以下步骤：（a）指定具有一组二面角对的固定数量的二次结构元件（b），产生包括所述次要结构元件的一组叠层; 和（c）评估所述堆叠的可设计性。

56. 发明申请

US20030138372A1 Method for identifying and synthesizing high dielectric constant perovskites 审中-公开
标题翻译：识别和合成高介电常数钙钛矿的方法
公开(公告)号：US20030138372A1
公开(公告)日：2003-07-24
申请号：US10185432
申请日：2002-06-28
申请人： The Research Foundation of State University of New York
发明人： Jonh B. Parise , Patrick M. Woodward , Jae-Hyun Park
IPC分类号： C01B019/00 , G06G007/48 , G06G007/58
CPC分类号： C01G23/002 , C01B13/14 , C01G19/006 , C01P2002/34 , C01P2002/72 , C01P2002/76 , C01P2002/77 , C01P2006/40
摘要： A method for forming stable structures which includes identifying compositions having a high probability of forming stable structures using predictive modeling and synthesizing the compositions under high pressure and high temperature conditions to form the stable structures. Preferred stable structures are perovskites having a three-dimensional framework of corner-linked MX6 octahedra. The predictive modeling allows evaluation of structural stabilities of given compositions while providing hypothetical molar volumes. It also estimates the molecular polarizability of the compositions from the atomic polarizabilities of its constituent ions. The predictive modeling also calculates the relative dielectric constant of the stable structures using the Clausius-Mossotti relationship and selects compositions having combinations of ions with complimentary ionic radii and bonding preferences. The synthesis of the identified compositions is carried out using high temperature and high pressure techniques to induce a structural transition of the composition to a denser phase.
摘要翻译：一种用于形成稳定结构的方法，其包括使用预测建模识别形成稳定结构的高概率的组合物，并在高压和高温条件下合成组合物以形成稳定的结构。优选的稳定结构是具有角连接的MX6八面体三维骨架的钙钛矿。预测模型允许评估给定组合物的结构稳定性，同时提供假设的摩尔体积。它还从其组成离子的原子极化率估计组合物的分子极化率。预测建模还使用克劳修斯 - 莫索蒂关系计算稳定结构的相对介电常数，并选择具有互补离子半径和键合偏好的离子组合的组合物。使用高温和高压技术进行鉴定的组合物的合成，以诱导组合物向较致密相的结构转变。

57. 发明申请

US20030125315A1 Probes, systems, and methods for drug discovery 审中-公开
标题翻译：用于药物发现的探针，系统和方法
公开(公告)号：US20030125315A1
公开(公告)日：2003-07-03
申请号：US10120278
申请日：2002-04-11
发明人： Adnan M. M. Mjalli , Chris Wysong , Jerome Baudry , Thomas Scott Yokum , Rob Andrews , William K. Banner
IPC分类号： G06G007/48 , G06G007/58 , G06F019/00 , G01N033/48 , G01N033/50 , A61K031/397 , A61K031/53
CPC分类号： C07D231/56 , A61K31/416 , A61K31/454 , C07C229/34 , C07C235/20 , C07C235/52 , C07C237/08 , C07C237/20 , C07C237/22 , C07C237/24 , C07C237/52 , C07C271/22 , C07C271/24 , C07C271/26 , C07C275/24 , C07C275/26 , C07C275/30 , C07C275/42 , C07C307/08 , C07C311/06 , C07C311/16 , C07C311/19 , C07C311/20 , C07C323/60 , C07C2601/08 , C07C2601/10 , C07C2601/14 , C07C2602/08 , C07C2602/10 , C07D207/09 , C07D231/12 , C07D237/04 , C07D243/08 , C07D243/14 , C07D249/12 , C07D277/38 , C07D307/20 , C07D307/52 , C07D309/10 , C07D309/14 , C07D335/02 , C07D407/12 , C07D409/12 , C07D417/04 , C40B40/04 , C40B50/14 , G01N33/53 , G01N33/94 , G01N2500/00 , G16B15/00 , G16B30/00 , G16C20/50
摘要： Aspects of the present invention include probes, methods, systems that have stand alone utility and may comprise features of a drug discovery system or method. The present invention also includes pharmaceutical compositions. In more detail, the present invention provides molecular probes and methods for producing molecular probes. The present invention provides also provides systems and methods for new drug discovery. An embodiment of the present invention utilizes sets of probes of the present invention and a new approach to computational chemistry in a drug discovery method having increased focus in comparison to heretofore utilized combinatorial chemistry. The present invention also provides computer software and hardware tools useful in drug discovery systems. In an embodiment of a drug discovery method of the present invention in silico methods and in biologico screening methods are both utilized to maximize the probability of success while minimizing the time and number of wet laboratory steps necessary to achieve the success.
摘要翻译：本发明的方面包括具有独立效用并且可以包括药物发现系统或方法的特征的探针，方法，系统。本发明还包括药物组合物。更详细地，本发明提供了用于产生分子探针的分子探针和方法。本发明还提供了用于新药物发现的系统和方法。与迄今使用的组合化学相比，本发明的一个实施例利用了本发明的探针组合和新的药物发现方法中的计算化学方法，其具有增加的焦点。本发明还提供了在药物发现系统中有用的计算机软件和硬件工具。在本发明的药物发现方法的一个实施方案中，在计算机方法和生物鉴别筛选方法中都被用来最大化成功的可能性，同时最小化实现成功所需的湿实验室步骤的时间和数量。

58. 发明申请

US20030115032A1 Language for networks 有权
标题翻译：网络语言
公开(公告)号：US20030115032A1
公开(公告)日：2003-06-19
申请号：US10288570
申请日：2002-11-04
发明人： Ron Maimon
IPC分类号： G06F017/27 , G06G007/48 , G06G007/58
CPC分类号： G06F17/2705 , G06F17/271
摘要： Presently described is a formal language for describing the function of biochemical networks. Because it is a language, it includes a method of parsing, or understanding the language, which is a highly complex recursive algorithm. This formal language, the Cell Language, is described both informally, so that it may be written, and formally, so that it may be parsed. The Cell Language makes it possible to model all the interactions in a cell in a single diagram, with only a few representations of each molecule. The notation is compact and modular, in the sense that complex interactions composed of many subparts may be annotated with the same symbols as the simplest interactions composed of individual molecules or genes.
摘要翻译：目前描述的是描述生物化学网络功能的正式语言。因为它是一种语言，它包括解析或理解语言的方法，这是一种高度复杂的递归算法。这种形式语言，细胞语言，非正式地被描述，以便它可以被书写并正式地被解析。单元语言使得可以在单个图中对单元格中的所有交互进行建模，只有每个分子的几个表示。符号是紧凑和模块化的，在某种意义上说，由许多子部分组成的复杂相互作用可以用与单个分子或基因组成的最简单的相互作用相同的符号进行注释。

59. 发明申请

US20030115030A1 Non-linear modelling of biological activity of chemical compounds 审中-公开
公开(公告)号：US20030115030A1
公开(公告)日：2003-06-19
申请号：US10025283
申请日：2001-12-19
申请人： Camitro Corporation
发明人： Todd J.A. Ewing
IPC分类号： G06G007/48 , G06G007/58
CPC分类号： C12Q1/26 , G16C20/30
摘要： Models predict activity of chemical compounds by employing nulltransformednull descriptor values. The descriptors are transformed via transformation functions that convert the raw descriptor values to new values better representing the contribution of the descriptors to the activity in question. Typically, these transformation functions are non-linear parametric functions such as Gaussian functions or sigmoid functions. Typically, the model will employ at least two different descriptors, each transformed by its own non-linear parametric function.

60. 发明申请

US20030113739A1 System of components for preparing oligonucleotides 审中-公开
标题翻译：制备寡核苷酸的组分体系
公开(公告)号：US20030113739A1
公开(公告)日：2003-06-19
申请号：US10116325
申请日：2002-04-04
发明人： Lex M. Cowsert , Brenda F. Baker , John McNeil , Susan M. Freier , Henri M. Sasmor , Douglas G. Brooks , Cara Ohashi , Jacqueline R. Wyatt , Alexander H. Borchers , Timothy A. Vickers
IPC分类号： C12Q001/68 , G06G007/48 , G06G007/58 , G06F019/00
CPC分类号： C12Q1/6811 , B01J2219/007 , C12N15/1048 , G16B20/00 , G16B30/00 , G16B35/00 , G16C20/60
摘要： Interative, preferably computer based iterative processes for generating synthetic compounds with desired physical, chemical and/or bioactive properties, i.e., active compounds, are provided. During iterations of the processes, a target nucleic acid sequence is provided or selected, and a library of candidate nucleobase sequences is generated in silico according to defined criteria. A nullvirtualnull oligonucleotide chemistry is chosen and a library of virtual oligonucleotide compounds having the selected nucleobase sequences is generated. These virtual compounds are reviewed and compounds predicted to have particular properties are selected. The selected compounds are robotically synthesized and are preferably robotically assayed for a desired physical, chemical or biological activity. Active compounds are thus generated and, at the same time, preferred sequences and regions of the target nucleic acid that are amenable to oligonucleotide or sequence-based modulation are identified.
摘要翻译：提供了用于产生具有期望的物理，化学和/或生物活性的合成化合物（即活性化合物）的相互优选的基于计算机的迭代方法。在该过程的迭代过程中，提供或选择靶核酸序列，并且根据确定的标准以计算机生成候选核碱基序列的文库。选择“虚拟”寡核苷酸化学，并产生具有选定的核碱基序列的虚拟寡核苷酸化合物文库。审查这些虚拟化合物，并选择预测具有特定性质的化合物。所选择的化合物是机械合成的，并且优选机械地测定所需的物理，化学或生物活性。因此产生活性化合物，并且同时确定适用于寡核苷酸或基于序列的调节的靶核酸的优选序列和区域。

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