Flexible mapping of homology onto structure with homolmapper.
Flexible mapping of homology onto structure with homolmapper.
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DOI：
10.1186/1471-2105-8-123
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发表时间：
2007-04-11
影响因子：
3
通讯作者：
Lagarias JC
中科院分区：
文献类型：
--
作者：
Rockwell NC;Lagarias JC
在过去的十年中，出现了一些工具，用于检查蛋白质序列之间的同源性关系的结构背景。用于这种分析的最新软件实现与特定的分子观察程序相关联，这对于涉及多个观察环境的协作来说可能是有问题的。合并到更大的软件包中也增加了用户感兴趣的复杂性，增加了自己的评分计划或分析蛋白质纳入不寻常的氨基酸残基，如硒代半胱氨酸。我们描述homolmapper，一个命令行应用程序，用于将来自多个蛋白质序列比对的信息映射到蛋白质结构上，以便在用户选择的查看软件中进行分析。Homolmapper很小（应用程序本身小于250 K），并且是用Python编写的，以确保可移植性。它是根据修改后的加州大学BSD许可证发布的非商业用途。Homolmapper允许容易地导入另外的评分方案，并且可以掺入任意的另外的氨基酸以允许处理残基如硒代半胱氨酸或吡咯赖氨酸。Homolmapper还提供了定义和分析相对于较大比对的亚家族的工具，用于互信息分析，以及用于快速可视化突变和多残基序的位置。Homolmapper是分析蛋白质结构中同源性关系的有效工具。还有大量的示例驱动文档可用。有关homolmapper的详细信息，请访问。
Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are tied to specific molecular viewing programs, which can be problematic for collaborations involving multiple viewing environments. Incorporation into larger packages also adds complications for users interested in adding their own scoring schemes or in analyzing proteins incorporating unusual amino acid residues such as selenocysteine. We describe homolmapper, a command-line application for mapping information from a multiple protein sequence alignment onto a protein structure for analysis in the viewing software of the user's choice. Homolmapper is small (under 250 K for the application itself) and is written in Python to ensure portability. It is released for non-commercial use under a modified University of California BSD license. Homolmapper permits facile import of additional scoring schemes and can incorporate arbitrary additional amino acids to allow handling of residues such as selenocysteine or pyrrolysine. Homolmapper also provides tools for defining and analyzing subfamilies relative to a larger alignment, for mutual information analysis, and for rapidly visualizing the locations of mutations and multi-residue motifs. Homolmapper is a useful tool for analysis of homology relationships among proteins in a structural context. There is also extensive, example-driven documentation available. More information about homolmapper is available at .
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
5.8
作者：
Glaser, F;Pupko, T;Ben-Tal, N
通讯作者：
Ben-Tal, N
影响因子：
2.9
作者：
Glaser, F;Rosenberg, Y;Ben-Tal, N
通讯作者：
Ben-Tal, N
DOI：
10.1002/prot.340230412
发表时间：
1995-12-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
Frishman, D;Argos, P
通讯作者：
Argos, P
DOI：
10.1073/pnas.0507266103
发表时间：
2006-01-03
影响因子：
11.1
作者：
Hagiwara, Y;Sugishima, M;Fukuyama, K
通讯作者：
Fukuyama, K