Journal Article

The trRosetta server for fast and accurate protein structure prediction

Ye, Lisha, Baker, David, Su, Hong, Anishchenko, Ivan, Yang, Jianyi, Wang, Wenkai, Du, Zongyang, Peng, Zhenling, Wei, Hong

2021

Overview

The trRosetta (transform-restrained Rosetta) server is a web-based platform for fast and accurate protein structure prediction, powered by deep learning and Rosetta. With the input of a protein’s amino acid sequence, a deep neural network is first used to predict the inter-residue geometries, including distance and orientations. The predicted geometries are then transformed as restraints to guide the structure prediction on the basis of direct energy minimization, which is implemented under the framework of Rosetta. The trRosetta server distinguishes itself from other similar structure prediction servers in terms of rapid and accurate de novo structure prediction. As an illustration, trRosetta was applied to two Pfam families with unknown structures, for which the predicted de novo models were estimated to have high accuracy. Nevertheless, to take advantage of homology modeling, homologous templates are used as additional inputs to the network automatically. In general, it takes ~1 h to predict the final structure for a typical protein with ~300 amino acids, using a maximum of 10 CPU cores in parallel in our cluster system. To enable large-scale structure modeling, a downloadable package of trRosetta with open-source codes is available as well. A detailed guidance for using the package is also available in this protocol. The server and the package are available at https://yanglab.nankai.edu.cn/trRosetta/ and https://yanglab.nankai.edu.cn/trRosetta/download/ , respectively. The trRosetta server, a web-based platform for fast and accurate protein structure prediction, is powered by deep learning and Rosetta. This protocol includes procedures for using the web-based server as well as the standalone package.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/114/2411 / 631/114/470 / Amino Acid Sequence / Amino acids / Amino Acids - chemistry / Analytical Chemistry / Artificial neural networks / Biological Techniques / Biomedical and Life Sciences / Computational Biology - methods / Computational Biology/Bioinformatics / Deep learning / Homology / Internet / Life Sciences / Machine learning / Methods / Microarrays / Modelling / Molecular Dynamics Simulation / Neural networks / Neural Networks, Computer / Organic Chemistry / Predictions / Protein Conformation, alpha-Helical / Protein Conformation, beta-Strand / Protein Interaction Domains and Motifs / Protein structure / Protein structure prediction / Proteins / Proteins - chemistry / Protocol / Servers / Software / Thermodynamics / Web applications