用序列文本动态参照协助生物分子3D结构观察

Assist inspection of biomolecular 3D structures using dynamic reference of sequence text

为了克服Jmol等传统工具在序列信息参照方式方面存在的缺陷,提出并实现了一种利用序列文本动态参照协助生物分子3D结构观察的方法.该方法利用Javascript,Frame,DIV,CSS,PHP和MySQL等Web相关技术,在Jmol基础上进行功能拓展.首先,分子序列文本与3D结构同时显示,且随着各种针对局部片段的操作同步发生变化.通过对序列文本特定编排以方便对局部片段的查看和定位,且利用下划线、删除线、上划线等多种文本样式及其配色来直观地表示多种局部操作结果状态.此外,还提供了多个序列片段的集中显示、历史操作状态的切换、当前状态的服务器保存等辅助功能.该方法在实际应用中取得了较好效果,有助于提升生物分子序列和结构相关生物信息的整合、模拟和可视化水平.

A method was presented to avoid the limitations of traditional tools such as Jmol in the ref- erence forms of sequence information using the dynamic reference of sequence text to assist the inspec tion of biomolecular 3D （three dimension） structures. In this method, Web related technologies such as Javascript, Frame, DIV, CSS, PHP and MySQL were used to extend the functions based on Jmol. Firstly, biomolecular sequence texts and 3D structures could be simultaneously displayed, and syn- chronously changed with the manipulations of molecular local regions. The sequence texts were spe- cially laid out to facilitate the view and location of local regions, and multiple text styles such as un- derline, strickout, overline along with their colors were used to represent multiple states from differ- ent local manipulations. In addition, some auxiliary functions were provided, including centralized display of multiple local regions in sequence, switch of historical manipulation states and save （to the server） of current state. This method shows satisfactory performance in practice, which is useful for improving the level of the integration, imitation and visualization of biomolecular sequence and struc- ture related bioinformation.