DePietro Paul J, Julfayev Elchin S, McLaughlin William A
Department of Basic Science, The Commonwealth Medical College, 525 Pine Street, Scranton, PA 18509, USA.
BMC Struct Biol. 2013 Oct 21;13:24. doi: 10.1186/1472-6807-13-24.
Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third phase entailed the formation of PSI:Biology Partnerships which are composed of structural genomics centers and biomedical science laboratories. We present a method to examine the impact of protein structures determined under the auspices of PSI:Biology by measuring their rates of annotations. The mean numbers of annotations per structure and per residue are examined. These are designed to provide measures of the amount of structure to function connections that can be leveraged from each structure.
One result is that PSI:Biology structures are found to have a higher rate of annotations than structures determined during the first two phases of PSI. A second result is that the subset of PSI:Biology structures determined through PSI:Biology Partnerships have a higher rate of annotations than those determined exclusive of those partnerships. Both results hold when the annotation rates are examined either at the level of the entire protein or for annotations that are known to fall at specific residues within the portion of the protein that has a determined structure.
We conclude that PSI:Biology determines structures that are estimated to have a higher degree of biomedical interest than those determined during the first two phases of PSI based on a broad array of biomedical annotations. For the PSI:Biology Partnerships, we see that there is an associated added value that represents part of the progress toward the goals of PSI:Biology. We interpret the added value to mean that team-based structural biology projects that utilize the expertise and technologies of structural genomics centers together with biological laboratories in the community are conducted in a synergistic manner. We show that the annotation rates can be used in conjunction with established metrics, i.e. the numbers of structures and impact of publication records, to monitor the progress of PSI:Biology towards its goals of examining structure to function connections of high biomedical relevance. The metric provides an objective means to quantify the overall impact of PSI:Biology as it uses biomedical annotations from external sources.
蛋白质结构计划：生物学（PSI：生物学）是PSI的第三阶段，在此阶段以高通量方式确定蛋白质结构以表征其生物学功能。向第三阶段的过渡需要组建PSI：生物学合作团队，这些团队由结构基因组学中心和生物医学科学实验室组成。我们提出了一种方法，通过测量蛋白质结构的注释率来检验在PSI：生物学支持下确定的蛋白质结构的影响。研究了每个结构和每个残基的平均注释数。这些旨在提供可从每个结构中利用的结构与功能联系数量的度量。
一个结果是，发现PSI：生物学结构的注释率高于PSI前两个阶段确定的结构。另一个结果是，通过PSI：生物学合作团队确定的PSI：生物学结构子集的注释率高于不通过这些合作团队确定的结构。当在整个蛋白质水平或已知落在具有确定结构的蛋白质部分内特定残基处的注释水平上检查注释率时，这两个结果均成立。
我们得出结论，基于广泛的生物医学注释，PSI：生物学确定的结构比PSI前两个阶段确定的结构具有更高程度的生物医学研究价值。对于PSI：生物学合作团队，我们发现存在相关的附加值，这代表了朝着PSI：生物学目标迈进的部分进展。我们将附加值解释为意味着利用结构基因组学中心的专业知识和技术以及社区中的生物实验室以协同方式开展基于团队的结构生物学项目。我们表明，注释率可与既定指标（即结构数量和发表记录的影响力）结合使用，以监测PSI：生物学在研究具有高生物医学相关性的结构与功能联系目标方面的进展。该指标提供了一种客观手段，可量化PSI：生物学利用外部来源的生物医学注释时的总体影响。
