School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK.
Nucleic Acids Res. 2021 Jul 2;49(W1):W425-W430. doi: 10.1093/nar/gkab321.
Methods for estimating the quality of 3D models of proteins are vital tools for driving the acceptance and utility of predicted tertiary structures by the wider bioscience community. Here we describe the significant major updates to ModFOLD, which has maintained its position as a leading server for the prediction of global and local quality of 3D protein models, over the past decade (>20 000 unique external users). ModFOLD8 is the latest version of the server, which combines the strengths of multiple pure-single and quasi-single model methods. Improvements have been made to the web server interface and there has been successive increases in prediction accuracy, which were achieved through integration of newly developed scoring methods and advanced deep learning-based residue contact predictions. Each version of the ModFOLD server has been independently blind tested in the biennial CASP experiments, as well as being continuously evaluated via the CAMEO project. In CASP13 and CASP14, the ModFOLD7 and ModFOLD8 variants ranked among the top 10 quality estimation methods according to almost every official analysis. Prior to CASP14, ModFOLD8 was also applied for the evaluation of SARS-CoV-2 protein models as part of CASP Commons 2020 initiative. The ModFOLD8 server is freely available at: https://www.reading.ac.uk/bioinf/ModFOLD/.
用于评估蛋白质 3D 模型质量的方法是推动更广泛的生物科学社区接受和利用预测的三级结构的重要工具。在这里，我们描述了 ModFOLD 的重大更新，该服务器在过去十年中（超过 20000 个独特的外部用户）一直保持着预测全局和局部 3D 蛋白质模型质量的领先服务器地位。ModFOLD8 是该服务器的最新版本，它结合了多种纯单模型和准单模型方法的优势。改进了网页服务器界面，并且通过整合新开发的评分方法和先进的基于深度学习的残基接触预测，预测准确性得到了提高。ModFOLD 服务器的每个版本都在两年一度的 CASP 实验中进行了独立的盲测，并且通过 CAMEO 项目不断进行评估。在 CASP13 和 CASP14 中，根据几乎所有官方分析，ModFOLD7 和 ModFOLD8 变体在质量评估方法中排名前十。在 CASP14 之前，ModFOLD8 还被用于评估 SARS-CoV-2 蛋白质模型，作为 CASP Commons 2020 计划的一部分。ModFOLD8 服务器可免费使用：https://www.reading.ac.uk/bioinf/ModFOLD/。
