2.软件与应用
MODELLER是一款同源模建软件[13]。其中，使用的原理就是基于空间约束的蛋白质结构预测。简而言之，软件的输入项是模板序列与目标序列的比对结果，模板序列的结构文件和脚本文件。然后，MODELLER就能自动计算出目标序列中所有非氢原子的坐标。MODELLER软件中涉及到的空间约束包括：同源约束，立体化学约束，统计约束和其他额外添加的约束。软件没有界面交互系统，只能通过脚本进行使用。
MODWEB是一种自动同源模建的网上服务器[14]。它接收一条以上的FASTA序列，然后在PDB数据库中搜索最可行的模板，并计算出提交的目标序列的模型。MODWEB使用的原理与MODELLER类似，只是在两个步骤进行了改进。它使用的模板搜索方法是序列结构比对，搜索使用的模板也不止一个。对于单个提交序列，MODWEB是通过邮件的形式返回结果。如果提交的序列不止一条或者包含结构时，返回的结果将被作为一个单独的数据集添加到蛋白质模型的相关数据集中。
3.展望
随着越来越多的蛋白质序列的三级结构被测定，同源模建的使用范围也不断扩大。其中，基于空间约束的同源模建方法是在所有同源模建方法中表现最好的方法。目前，对基于空间约束的同源模建方法的研究也越来越深入。许多额外的实验数据约束被添加到方法中来，比如，核磁共振数据，交联试验数据，荧光光谱实验数据，微电子图像重建实验数据和定点突变实验数据。实验数据约束的添加使基于空间约束的同源模建方法的预测结果更加的合理。
总之，基于空间约束的同源模建方法具有能添加多种来源的数据约束的特点，是同源模建方法中与实验数据联系最深的方法，也意味着是最有潜力的方法。
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