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US5436850A Method to identify protein sequences that fold into a known three-dimensional structure 失效
标题翻译：鉴定折叠成已知三维结构的蛋白质序列的方法
公开(公告)号：US5436850A
公开(公告)日：1995-07-25
申请号：US218685
申请日：1994-03-28
申请人： David Eisenberg , James U. Bowie , Roland Luthy
发明人： David Eisenberg , James U. Bowie , Roland Luthy
IPC分类号： C07K1/00 , G01N33/68 , G06F17/50 , G06F19/00 , C12Q1/68
CPC分类号： G06F19/16 , C07K1/00 , G01N33/68
摘要： A computer-assisted method for identifying protein sequences that fold into a known three-dimensional structure. The inventive method attacks the inverse protein folding problem by finding target sequences that are most compatible with profiles representing the structural environments of the residues in known three-dimensional protein structures. The method starts with a known three-dimensional protein structure and determines three key features of each residue's environment within the structure: (1) the total area of the residue's side-chain that is buried by other protein atoms, inaccessible to solvent; (2) the fraction of the side-chain area that is covered by polar atoms (O, N) or water, and (3) the local secondary structure. Based on these parameters, each residue position is categorized into an environment class. In this manner, a three-dimensional protein structure is converted into a one-dimensional environment string, which represents the environment class of each residue in the folded protein structure. A 3D structure profile table is then created containing score values that represent the frequency of finding any of the 20 common amino acids structures at each position of the environment string. These frequencies are determined from a database of known protein structures and aligned sequences. The method determines the most favorable alignment of a target protein sequence to the residue positions defined by the environment string, and determines a "best fit" alignment score, S.sub.ij, for the target sequence. Each target sequence may then be further characterized by a ZScore, which is the number of standard deviations that S.sub.ij for the target sequence is above the mean alignment score for other target sequences of similar length.
摘要翻译：用于鉴定折叠成已知三维结构的蛋白质序列的计算机辅助方法。本发明的方法通过找到与表示已知三维蛋白质结构中的残基的结构环境的图谱最相容的靶序列来攻击逆蛋白质折叠问题。该方法从已知的三维蛋白质结构开始，确定结构内每个残基环境的三个关键特征：（1）被其他蛋白质原子掩埋的残留物侧链的总面积，溶剂不可及; （2）由极性原子（O，N）或水覆盖的侧链区域的分数，以及（3）局部二级结构。基于这些参数，每个残差位置被分类为一个环境类。以这种方式，将三维蛋白质结构转化为一维环境串，其代表折叠的蛋白质结构中每个残基的环境类别。然后创建3D结构简档表，其中包含表示在环境字符串的每个位置找到20个常见氨基酸结构中的任何一个的频率的评分值。这些频率由已知蛋白质结构和比对序列的数据库确定。该方法确定目标蛋白质序列与由环境序列定义的残基位置的最佳比对，并确定靶序列的“最佳拟合”比对分数Sij。然后可以通过ZScore进一步表征每个靶序列，ZScore是靶序列的Sij高于具有相似长度的其他靶序列的平均比对分数的标准偏差数。

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