CORDAX 网络服务器:用于预测蛋白质序列中聚集图案并将其三维可视化的在线平台。

IF 4.4 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Bioinformatics Pub Date : 2024-04-25 DOI:10.1093/bioinformatics/btae279
Nikolaos N. Louros, F. Rousseau, J. Schymkowitz
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引用次数: 0

摘要

动因蛋白质是生物系统的分子主力,根据其精确的三维结构执行多种关键功能。在复杂多变的细胞环境中,蛋白质会发生错误折叠,从而形成各种形式的聚集体,包括淀粉样纤维状的无定形聚集体和有序聚集体。这种现象与阿尔茨海默病、帕金森病、II 型糖尿病和其他几种蛋白质疾病等一系列广泛的衰弱性病症密切相关,同时也阻碍了可溶性制剂的工程设计,例如抗体的开发。因此,准确预测蛋白质序列中的聚集倾向已变得至关重要,因为这对了解疾病机制以及改进生物技术和治疗应用具有深远影响。在此,我们介绍了 Cordax 的专用网络服务器界面。该在线平台集多种功能于一体,包括序列聚集倾向的详细评分,以及三维可视化,并为预测聚集图案形成的结构核心拓扑模型提供了多种自定义选项。此外,该平台还提供实验确定的易聚集区域的信息,这些区域与预测图案的序列具有相似性、得分、与其他预测器输出结果的链接,以及相关序列倾向性的同步预测,如溶解性、疏水性和二级结构倾向性。
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CORDAX web server: An online platform for the prediction and 3D visualization of aggregation motifs in protein sequences.
MOTIVATION Proteins, the molecular workhorses of biological systems, execute a multitude of critical functions dictated by their precise three-dimensional structures. In a complex and dynamic cellular environment, proteins can undergo misfolding, leading to the formation of aggregates that take up various forms, including amorphous and ordered aggregation in the shape of amyloid fibrils. This phenomenon is closely linked to a spectrum of widespread debilitating pathologies, such as Alzheimer's disease, Parkinson's disease, type-II diabetes, and several other proteinopathies, but also hampers the engineering of soluble agents, as in the case of antibody development. As such, the accurate prediction of aggregation propensity within protein sequences has become pivotal due to profound implications in understanding disease mechanisms, as well as in improving biotechnological and therapeutic applications. RESULTS We previously developed Cordax, a structure-based predictor that utilizes logistic regression to detect aggregation motifs in protein sequences based on their structural complementarity to the amyloid cross-beta architecture. Here, we present a dedicated web server interface for Cordax. This online platform combines several features including detailed scoring of sequence aggregation propensity, as well as 3D visualization with several customization options for topology models of the structural cores formed by predicted aggregation motifs. In addition, information is provided on experimentally determined aggregation-prone regions that exhibit sequence similarity to predicted motifs, scores, and links to other predictor outputs, as well as simultaneous predictions of relevant sequence propensities, such as solubility, hydrophobicity, and secondary structure propensity. AVAILABILITY The Cordax webserver is freely accessible at https://cordax.switchlab.org/.
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来源期刊
Bioinformatics
Bioinformatics 生物-生化研究方法
CiteScore
11.20
自引率
5.20%
发文量
753
审稿时长
2.1 months
期刊介绍: The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.
期刊最新文献
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