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1.发明申请公开(公告)号：US20050119835A1
公开(公告)日：2005-06-02
申请号：US10967011
申请日：2004-10-14
申请人： David Kita , Somalee Datta , Adityo Prakash , Eniko Fodor
发明人： David Kita , Somalee Datta , Adityo Prakash , Eniko Fodor
IPC分类号： C12Q1/00 , C12Q1/68 , G01N33/48 , G01N33/50 , G06F20060101 , G06F19/16 , G06F19/18 , G06F19/24 , G06F19/26 , G06F19/00
CPC分类号： G06F19/16 , G06F19/18 , G06F19/24 , G06F19/26 , G06F19/706
摘要： A method and apparatus for analysis of molecular combinations featuring two or more molecular subsets is described. The computational method estimates the electrostatic affinity of the system via utilization of a basis expansion representing charge density and electrostatic potential functions associated with the first and second molecular subsets in a coordinate system. An electrostatic affinity, representing a correlation of the charge density and electrostatic potential functions of the first and second molecular subsets, is computed via suitable application of translation and rotation operators to the basis expansion coefficients over a sequence of different sampled configurations for the molecular combination. The method may also be combined with other methods for computation of shape complementarity in determining a composite or augmented score reflecting both electrostatic affinity and shape complementarity for configurations of a molecular combination.
摘要翻译： 描述用于分析具有两个或更多个分子子集的分子组合的方法和装置。 计算方法通过利用表示电荷密度的基础膨胀和与坐标系中的第一和第二分子子集相关联的静电势函数来估计系统的静电亲和力。 表示第一和第二分子子集的电荷密度和静电势函数的相关性的静电亲和力是通过对分子组合的不同采样配置的序列的基础扩展系数的适当应用来计算的。 该方法还可以与用于计算形状互补性的其它方法组合，以确定反映分子组合构型的静电亲和力和形状互补性的复合或增强分数。
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2.发明申请公开(公告)号：US20050119834A1
公开(公告)日：2005-06-02
申请号：US10966160
申请日：2004-10-14
申请人： David Kita , Somalee Datta , Adityo Prakash , Eniko Fodor
发明人： David Kita , Somalee Datta , Adityo Prakash , Eniko Fodor
CPC分类号： G06F19/16 , G06F19/24 , G06F19/706
摘要： A method and apparatus for analysis of molecular combinations featuring two or more molecular subsets is described. The method computes the shape complementarity of the system utilizing a basis expansion representing molecular shapes of the first and second molecular subsets in a coordinate system. The precomputed sets of translated expansion coefficients for the first molecular subset are first constructed via application of a translation operator to a reference set of expansion coefficients and then stored on a computer recordable medium for later retrieval. Then a shape complementarity score, representing a correlation of the first and second molecular subsets, is computed via suitable application of rotation operators to both the stored translated expansion coefficients of the first molecular subset, and the reference expansion coefficients for the second molecular subset, over the sequence of different sampled configurations for the molecular combination. The application of a translation operator prior to one or more rotation operator(s) has significant and beneficial implications for hardware-based implementations of the method, embodiments of which in the context of a hardware apparatus will also be described.
摘要翻译： 描述用于分析具有两个或更多个分子子集的分子组合的方法和装置。 该方法利用表示坐标系中第一和第二分子子集的分子形状的基础扩展来计算系统的形状互补性。 首先通过将翻译算子应用于扩展系数的参考集合来构建用于第一分子子集的经翻译的扩展系数的预先计算的集合，然后存储在计算机可记录介质上用于稍后检索。 然后，表示第一和第二分子子集的相关性的形状互补评分通过将旋转算子适当地应用于第一分子子集的存储的翻译扩展系数和第二分子子集的参考扩增系数， 分子组合的不同采样配置的序列。 翻译运算符在一个或多个旋转运算符之前的应用对于该方法的基于硬件的实现具有显着和有益的影响，还将描述其硬件装置的上下文中的实施例。
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3.发明授权公开(公告)号：US07890313B2
公开(公告)日：2011-02-15
申请号：US10966160
申请日：2004-10-14
申请人： David Kita , Somalee Datta , Adityo Prakash , Eniko Fodor
发明人： David Kita , Somalee Datta , Adityo Prakash , Eniko Fodor
CPC分类号： G06F19/16 , G06F19/24 , G06F19/706
摘要： A method and apparatus for analysis of molecular combinations featuring two or more molecular subsets is described. The method computes the shape complementarity of the system utilizing a basis expansion representing molecular shapes of the first and second molecular subsets in a coordinate system. The precomputed sets of translated expansion coefficients for the first molecular subset are first constructed via application of a translation operator to a reference set of expansion coefficients and then stored on a computer recordable medium for later retrieval. Then, a shape complementarity score, representing a correlation of the first and second molecular subsets, is computed via suitable application of rotation operators to both the stored translated expansion coefficients of the first molecular subset and the reference expansion coefficients for the second molecular subset over the sequence of different sampled configurations for the molecular combination.
摘要翻译： 描述用于分析具有两个或更多个分子子集的分子组合的方法和装置。 该方法利用表示坐标系中第一和第二分子子集的分子形状的基础扩展来计算系统的形状互补性。 首先通过将翻译算子应用于扩展系数的参考集合来构建用于第一分子子集的经翻译的扩展系数的预先计算的集合，然后存储在计算机可记录介质上用于稍后检索。 然后，代表第一和第二分子子集的相关性的形状互补评分通过将旋转算子适当地应用于第一分子子集的存储的翻译扩展系数和第二分子子集的参考扩增系数 用于分子组合的不同采样配置的序列。
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公开(公告)号：US06970790B2
公开(公告)日：2005-11-29
申请号：US10967011
申请日：2004-10-14
申请人： David Kita , Somalee Datta , Adityo Prakash , Eniko Fodor
发明人： David Kita , Somalee Datta , Adityo Prakash , Eniko Fodor
IPC分类号： C12Q1/00 , C12Q1/68 , G01N33/48 , G01N33/50 , G06F20060101 , G06F19/16 , G06F19/18 , G06F19/24 , G06F19/26
CPC分类号： G06F19/16 , G06F19/18 , G06F19/24 , G06F19/26 , G06F19/706
摘要： A method and apparatus for analysis of molecular combinations featuring two or more molecular subsets is described. The computational method estimates the electrostatic affinity of the system via utilization of a basis expansion representing charge density and electrostatic potential functions associated with the first and second molecular subsets in a coordinate system. An electrostatic affinity, representing a correlation of the charge density and electrostatic potential functions of the first and second molecular subsets, is computed via suitable application of translation and rotation operators to the basis expansion coefficients over a sequence of different sampled configurations for the molecular combination. The method may also be combined with other methods for computation of shape complementarity in determining a composite or augmented score reflecting both electrostatic affinity and shape complementarity for configurations of a molecular combination.
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5.发明申请公开(公告)号：US20120116742A1
公开(公告)日：2012-05-10
申请号：US13253035
申请日：2011-10-04
申请人： Adityo Prakash , David Kita , Eniko Fodor
发明人： Adityo Prakash , David Kita , Eniko Fodor
IPC分类号： G06G7/48
摘要： Method and apparatus for the efficient computation of values for affinity functions for two or more molecular subsets of a molecular configuration, are provided. Either one or both of molecular subsets may be selected from a molecule library. Affinity engines can compute the affinity values, and can be synchronized in order to maximize utilization of processing power available in the affinity engines. A data path allocator can apportion molecular descriptor data to each affinity engine as one or more data blocks according to a data path schedule. Also, new configurations may be generated from one or more input configurations, computation of a plurality of affinity values for a plurality of configurations, and subsequent selection of processed configurations for further analysis.
摘要翻译： 提供了用于有效计算分子构型的两个或多个分子子集的亲和力函数的值的方法和装置。 分子亚类中的任一个或两个可以选自分子文库。 亲和引擎可以计算亲和力值，并且可以同步，以最大限度地利用亲和力引擎中可用的处理能力。 数据路径分配器可以根据数据路径调度将分子描述符数据分配给每个亲和力引擎作为一个或多个数据块。 此外，可以从一个或多个输入配置，多个配置的多个亲和度值的计算以及随后选择用于进一步分析的经处理的配置来生成新的配置。
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6.发明授权公开(公告)号：US08036867B2
公开(公告)日：2011-10-11
申请号：US10967085
申请日：2004-10-14
申请人： Adityo Prakash , David Kita , Eniko Fodor
发明人： Adityo Prakash , David Kita , Eniko Fodor
摘要： Computing units are determined for performing molecular docking calculations in parallel with the number of computing units and the width of the data paths allocated by relative complexity of operations. Data can be expected to arrive at downstream computing units as it is needed, leading to higher utilization of computing units. Computing units are hardware components that are specific to a calculation performed. For molecular docking calculations, functions of molecular subsets or of combinations of molecular subsets are calculated. Determinations include fit between molecular subsets, affinity or energy of “fit” between molecular subsets, etc. Affinity might include inter-atomic energy, bond energy, energy of atoms immersed in a field, etc. The calculations could be used to simulate and/or estimate likelihoods of molecular interactions.
摘要翻译： 确定计算单元与计算单元的数量和通过操作的相对复杂度分配的数据路径的宽度并行执行分子对接计算。 数据可以预期在需要时到达下游计算单元，导致计算单元的更高利用率。 计算单位是特定于执行计算的硬件组件。 对于分子对接计算，计算分子子集的功能或分子子集的组合。 测定包括分子亚群之间的拟合，分子子集之间的“拟合”的亲和力等等。亲和性可以包括原子间能量，键能，浸在场中的原子的能量等。计算可以用于模拟和/ 或估计分子相互作用的可能性。
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公开(公告)号：US20050228592A1
公开(公告)日：2005-10-13
申请号：US10966041
申请日：2004-10-14
申请人： Sachin Ahuja , David Kita , Eniko Fodor , Adityo Prakash
发明人： Sachin Ahuja , David Kita , Eniko Fodor , Adityo Prakash
IPC分类号： C12Q1/68 , G01N20060101 , G01N33/48 , G01N33/50 , G01N33/68 , G06F7/00 , G06F19/00 , G06F19/16 , G06F19/18 , G06G7/48
CPC分类号： G06F19/701 , C40B30/02 , G01N33/6803 , G06F19/16 , G06F19/18 , G06F19/24 , G06F19/26 , G06F19/28 , G06F19/706 , G06F19/707
摘要： A method for partitioning a molecular subset is described. The partitioning method takes into account molecular structure and its manner of storage and transmission, transformations to be applied to the molecular subset and their implementation, and constraints imposed by the implementation of the partitioning method. Using this method, a molecular subset can be stored, transmitted, and processed more efficiently. The resulting efficiency makes it possible to design and run applications which require complex molecular processing, such as rational drug discovery, virtual library design, etc.
摘要翻译： 描述了用于分割分子子集的方法。 分割方法考虑了分子结构及其存储和传输方式，应用于分子子集的变换及其实现，以及实施分区方法所施加的约束。 使用这种方法，可以更有效地存储，传输和处理分子子集。 所产生的效率使得可以设计和运行需要复杂的分子处理的应用，例如合理的药物发现，虚拟图书馆设计等。
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公开(公告)号：US20050170379A1
公开(公告)日：2005-08-04
申请号：US10966341
申请日：2004-10-14
申请人： David Kita , Eniko Fodor , Adityo Prakash
发明人： David Kita , Eniko Fodor , Adityo Prakash
IPC分类号： C12Q1/68 , G01N33/48 , G01N33/50 , G01N33/569 , G01N33/68 , G05B15/00 , G06F20060101 , G06F19/00 , G06F19/16
CPC分类号： G01N33/6803 , G01N2500/00 , G06F19/16 , G06F19/702
摘要： A method for the prediction of adverse cross-reactions between lead candidate biomolecules and potential reactant molecules, often biopolymers, is described. In a computational system, reactions are modeled within a suitable environment, in order to determine a reaction profile between a lead candidate molecule and a potential reactant molecule. A risk assessment is then generated for each lead based on a plurality of reaction profiles for the lead with respect to a plurality of potential reactant molecules. The method includes provisions for redesign and optimization of the lead candidate, possibly iterative in nature, in order to avoid predicted adverse cross-reactions.
摘要翻译： 描述了用于预测潜在候选生物分子与潜在的反应物分子（通常是生物聚合物）之间的不利交叉反应的方法。 在计算系统中，在合适的环境内对反应进行建模，以便确定主要候选分子和潜在的反应物分子之间的反应分布。 然后基于针对多个潜在的反应物分子的多个反应曲线，为每个引线产生风险评估。 该方法包括重新设计和优化主要候选人的条款，可能是迭代性质的，以避免预测的不利交叉反应。
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公开(公告)号：US09317664B2
公开(公告)日：2016-04-19
申请号：US10966041
申请日：2004-10-14
申请人： Sachin Ahuja , David Kita , Eniko Fodor , Adityo Prakash
发明人： Sachin Ahuja , David Kita , Eniko Fodor , Adityo Prakash
IPC分类号： G01N33/48 , G01N33/50 , G06F19/00 , G06F19/24 , G06F19/26 , G06F19/28 , G01N33/68 , G06F19/16 , C40B30/02 , G06F19/18
CPC分类号： G06F19/701 , C40B30/02 , G01N33/6803 , G06F19/16 , G06F19/18 , G06F19/24 , G06F19/26 , G06F19/28 , G06F19/706 , G06F19/707
摘要： A method for partitioning a molecular subset is described. The partitioning method takes into account molecular structure and its manner of storage and transmission, transformations to be applied to the molecular subset and their implementation, and constraints imposed by the implementation of the partitioning method. Using this method, a molecular subset can be stored, transmitted, and processed more efficiently. The resulting efficiency makes it possible to design and run applications which require complex molecular processing, such as rational drug discovery, virtual library design, etc.
摘要翻译： 描述了用于分割分子子集的方法。 分割方法考虑了分子结构及其存储和传输方式，应用于分子子集的变换及其实现，以及实施分区方法所施加的约束。 使用这种方法，可以更有效地存储，传输和处理分子子集。 所产生的效率使得可以设计和运行需要复杂的分子处理的应用，例如合理的药物发现，虚拟图书馆设计等。
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公开(公告)号：US07751988B2
公开(公告)日：2010-07-06
申请号：US10966341
申请日：2004-10-14
申请人： David Kita , Eniko Fodor , Adityo Prakash
发明人： David Kita , Eniko Fodor , Adityo Prakash
CPC分类号： G01N33/6803 , G01N2500/00 , G06F19/16 , G06F19/702
摘要： A method for the prediction of adverse cross-reactions between lead candidate biomolecules and potential reactant molecules, often biopolymers, is described. In a computational system, reactions are modeled within a suitable environment, in order to determine a reaction profile between a lead candidate molecule and a potential reactant molecule. A risk assessment is then generated for each lead based on a plurality of reaction profiles for the lead with respect to a plurality of potential reactant molecules. The method includes provisions for redesign and optimization of the lead candidate, possibly iterative in nature, in order to avoid predicted adverse cross-reactions.
摘要翻译： 描述了用于预测潜在候选生物分子与潜在的反应物分子（通常是生物聚合物）之间的不利交叉反应的方法。 在计算系统中，在合适的环境内对反应进行建模，以便确定主要候选分子和潜在的反应物分子之间的反应分布。 然后基于针对多个潜在的反应物分子的多个反应曲线，为每个引线产生风险评估。 该方法包括重新设计和优化主要候选人的条款，可能是迭代性质的，以避免预测的不利交叉反应。
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