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    • 6. 发明申请
    • A METHOD AND SYSTEM FOR THE PREDICTION OF A 3D STRUCTURE OF A TRANSMEMBRANE PROTEIN
    • 一种用于预测转运蛋白3D结构的方法和系统
    • WO0215106A2
    • 2002-02-21
    • PCT/IL0100768
    • 2001-08-16
    • UNIV RAMOTBECKER OREN MNAOR ZVISHACHAM SHARONTOPF MAYA
    • BECKER OREN MNAOR ZVISHACHAM SHARONTOPF MAYA
    • G06F19/16G06F19/00
    • G06F19/16
    • The present invention relates to a method for predicting the three-dimensional (3D) structure of a multiple a-helical transmembrane (TM) protein or a portion thereof having multiple helical TM helices, whereby each helical region is represented as a (2D) dial, and the weighted hydrophobicity moment of each (2D) dial is calculated. Closed packing geometries are constructed in which the dials are ordered according to predetermined topologies. For each closed packing geometry, each dial is rotated around its axis so that the weighted hydrophobicity moment faces out from the packing geometry. Each rotated (2D) closed packing geometry is expanded into a corresponding reduced (3D) representation, and the reduced (3D) representation with the lowest total energy is determined. Further provided by the present invention is a computer based system, a computer program storage device readable by machine and a computer program product for the execution of the method of the invention.
    • 本发明涉及一种用于预测多个α-螺旋跨膜(TM)蛋白质或其多个螺旋TM螺旋的部分的三维(3D)结构的方法,其中每个螺旋区域表示为(2D)刻度盘 ,并计算每个(2D)刻度盘的加权疏水力矩。 构建封闭的几何形状,其中根据预定的拓扑结构对刻度盘进行排序。 对于每个封闭的包装几何形状,每个表盘围绕其轴线旋转,使得加权的疏水性力矩从包装几何形状出发。 每个旋转的(2D)封闭填充几何扩展为相应的缩小(3D)表示,并且确定具有最低总能量的缩小(3D)表示。 本发明还提供了一种基于计算机的系统,可由机器读取的计算机程序存储装置和用于执行本发明的方法的计算机程序产品。
    • 7. 发明申请
    • METHOD AND SYSTEM FOR PREDICTING AMINO ACID SEQUENCE
    • 用于预测氨基酸序列的方法和系统
    • WO0214875A3
    • 2003-02-27
    • PCT/IL0100769
    • 2001-08-16
    • UNIV RAMOTBECKER OREN MTOPF MAYA
    • BECKER OREN MTOPF MAYA
    • G01N33/68G06F19/16G06F17/50G06F19/00
    • G06F19/16G01N33/6803
    • A method for predicting an amino acid sequence compatible with a three-dimensional (3D) structure of a protein is provided by the present invention. In general, a reduced virtual representation of the 3D structure is constructed, and, for each position along the representation, its solvent accessibility is determined. For each position along the structure, an amino acid residue is randomly selected from a predefined group of amino acids having a solvent accessibility compatible with the solvent accessibility of the position. A Monte-Carlo simulation is performed on this devised protein in which an amino acid at a particular position is sequentially replaced with other amino acids having the same solvent accessibility, and an energy score is calculated for each rotamer. The lowest scoring rotamer for this position is then selected The Monte-Carlo simulation is repeated for each position along the sequence, to obtain an amino acid sequence with the lowest total energy score. The invention also provides a computer based system, a computer program storage device readable by machine and a computer program product utilized for the execution of the method of the invention.
    • 本发明提供了一种用于预测与蛋白质的三维(3D)结构相容的氨基酸序列的方法。 通常,构造3D结构的减少的虚拟表示,并且对于沿着表示的每个位置,确定其溶剂可访问性。 对于沿着结构的每个位置,氨基酸残基从预定义的氨基酸组中随机选择,其具有与该位置的溶剂可及性相容的溶剂可及性。 对该设计蛋白质进行Monte-Carlo模拟,其中特定位置的氨基酸被顺序地替换为具有相同溶剂可及性的其它氨基酸,并计算每个旋转异构体的能量分数。 然后选择该位置的最低得分旋转异构体对沿着序列的每个位置重复蒙特卡罗模拟,以获得具有最低总能量分数的氨基酸序列。 本发明还提供了一种基于计算机的系统,由机器可读的计算机程序存储装置和用于执行本发明的方法的计算机程序产品。