The trRosetta server for fast and accurate protein structure prediction
| Autor: | Wenkai Wang, Hong Su, Zongyang Du, Ivan Anishchenko, Zhenling Peng, Hong Wei, David Baker, Lisha Ye, Jianyi Yang |
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| Rok vydání: | 2021 |
| Předmět: |
Protein Conformation
alpha-Helical Computer science Download Molecular Dynamics Simulation Energy minimization General Biochemistry Genetics and Molecular Biology Computational science Server Protein Interaction Domains and Motifs Amino Acid Sequence Amino Acids Protocol (object-oriented programming) Internet Multi-core processor Artificial neural network business.industry Deep learning Computational Biology Proteins Protein structure prediction Thermodynamics Protein Conformation beta-Strand Neural Networks Computer Artificial intelligence business Software |
| Zdroj: | Nature Protocols. 16:5634-5651 |
| ISSN: | 1750-2799 1754-2189 |
| DOI: | 10.1038/s41596-021-00628-9 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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