公开(公告)号：EP2973132A4

公开(公告)日：2017-01-25

申请号：EP14762610

申请日：2014-03-13

申请人： ZYMEWORKS INC

发明人： LAKATOS GREGORY ,  MCWHIRTER JAMES LIAM

IPC分类号： G06F19/10 ,  C07K1/00 ,  C12P21/00

CPC分类号： G06F17/5009 ,  G06F17/10 ,  G06F19/16

摘要： Systems and methods for evaluating thermodynamics of atomic changes in a polymer include using a first portion of a refined derived set of three-dimensional coordinates for a derivation of the polymer, which incorporates the atomic change under study, to compute a first effective atomistic Hessian. A second effective atomistic Hessian is computed using a second portion of a refined native set of three-dimensional coordinates for the native polymer. Atoms in the first and second portions are identical. A thermodynamic property of the first portion is determined using the refined derived set of three-dimensional coordinates and the first effective atomistic Hessian. A thermodynamic property of the second portion of the native polymer is determined using the refined native set of three-dimensional coordinates and the second effective atomistic Hessian. The effect of the atomic changes is quantified by taking the difference between the calculated thermodynamic properties of the first and second portions.

摘要翻译： 系统和用于评价的在聚合物原子更改热力学方法包括使用一个精制衍生集的三维坐标中的第一部分，用于聚合物，结合有原子变更替补的推导，来计算的第一有效原子论Hessian矩阵。 第二有效原子论的Hessian使用精制天然组用于天然聚合物的三维坐标中的第二部分来计算。 在第一和第二部分的原子是相同的。 所述第一部分的热力学性质是使用三维坐标的精衍生的集合和所述第一有效原子论海森确定性开采。 天然聚合物的第二部分的热力学性质是使用三维坐标的精制天然集合和第二有效原子论海森确定性开采。 的原子变化的影响是通过取第一和第二部分的计算的热力学性质之间的差异进行量化。

公开(公告)号：EP2864917A4

公开(公告)日：2015-12-16

申请号：EP13807096

申请日：2013-06-21

申请人： ZYMEWORKS INC

发明人： LAKATOS GREGORY ,  SRINIVASAN SIDDHARTH ,  DIXIT SURJIT BHIMARAO

IPC分类号： G06F19/16 ,  C07K1/00 ,  C40B30/02 ,  G01N33/68 ,  G06F19/00

CPC分类号： G06F19/16 ,  C07K1/00 ,  C07K2299/00 ,  G01N33/68 ,  G06F19/704 ,  G06F19/707

摘要： Systems, methods and non-transitory computer readable media identify favored polymer conformations. One or more residues are identified and may be replaced in the polymer, or the original primary sequence of the polymer may be retained. The conformations of residues in a subset of residues in a region of the identified one or more residues are altered. This conformational adjustment is repeated for other subsets of residues in the region of the identified one or more residues, and for other conformations, thereby deriving a plurality of polymer structures. A set of clusters is generated for each residue of the polymer using the conformationally adjusted structures, thereby creating sets of clusters. Structures in the plurality of structures are grouped into subgroups when the structures fall into the same clusters across a threshold number of the sets of clusters. One or more physical properties are determined for structures in subgroups, thereby identifying one or more thermodynamically relevant polymer conformations for the polymer.

公开(公告)号：EP2622524A4

公开(公告)日：2014-12-24

申请号：EP11827860

申请日：2011-09-29

申请人： ZYMEWORKS INC

发明人： OHRN ANDERS ,  LAKATOS GREGORY

IPC分类号： G06F19/10 ,  C07K1/00 ,  C12P21/00

CPC分类号： G06F19/24 ,  C07K1/00 ,  G06F19/16

摘要： The invention provides a method of determining changes in a first set of residues r1 due to changes in a second set of residues r2 in a protein system comprising one or more proteins comprising n and r2. In exemplary embodiments, the method comprises optimizing a quality function Q by modifying one or more properties of r1 and r2 in a constrained environment in which all degrees of freedom of the system except those directly involved in the potential coupling between r1 and r2 are removed.

摘要翻译： 本发明提供了一种确定由于包含一种或多种包含n和r2的蛋白质的蛋白质系统中第二组残基r2引起的第一组残基r1的变化的方法。 在示例性实施例中，该方法包括通过在受限环境中修改r1和r2的一个或多个属性来优化质量函数Q，其中除了直接涉及r1和r2之间的电势耦合的那些系统的所有自由度都被去除。