Biozentrum, University of Basel, Basel, Switzerland.
SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
PLoS Comput Biol. 2021 Jan 28;17(1):e1008667. doi: 10.1371/journal.pcbi.1008667. eCollection 2021 Jan.
Computational methods for protein structure modelling are routinely used to complement experimental structure determination, thus they help to address a broad spectrum of scientific questions in biomedical research. The most accurate methods today are based on homology modelling, i.e. detecting a homologue to the desired target sequence that can be used as a template for modelling. Here we present a versatile open source homology modelling toolbox as foundation for flexible and computationally efficient modelling workflows. ProMod3 is a fully scriptable software platform that can perform all steps required to generate a protein model by homology. Its modular design aims at fast prototyping of novel algorithms and implementing flexible modelling pipelines. Common modelling tasks, such as loop modelling, sidechain modelling or generating a full protein model by homology, are provided as production ready pipelines, forming the starting point for own developments and enhancements. ProMod3 is the central software component of the widely used SWISS-MODEL web-server.
蛋白质结构建模的计算方法通常用于补充实验结构测定，从而有助于解决生物医学研究中广泛的科学问题。目前最准确的方法基于同源建模，即检测到与所需目标序列具有同源性的序列，该序列可作为建模的模板。在这里，我们提出了一个通用的开源同源建模工具包，作为灵活且计算高效的建模工作流程的基础。ProMod3 是一个完全可脚本化的软件平台，可以执行通过同源建模生成蛋白质模型所需的所有步骤。其模块化设计旨在快速原型设计新算法并实现灵活的建模管道。常见的建模任务，如环建模、侧链建模或通过同源建模生成完整的蛋白质模型，都作为生产就绪的管道提供，为自主开发和增强提供了起点。ProMod3 是广泛使用的 SWISS-MODEL 网络服务器的核心软件组件。
