ReviewNature protocols2021
The trRosetta server for fast and accurate protein structure prediction.
Review in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 346 papers.
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Who cites it
346 citing papers in PubMed.
- The SLC-ome of membrane transport: from molecular discovery to physiology and clinical applications.Physiological reviews · 2026Review
- The trRosettaRNA server for RNA structure prediction.Nature protocols · 2026Review
- A Quantum-Classical Analysis of Variability in Peptide Energies and Conformations.The protein journal · 2026Article
- Adaptive variation in butyrylcholinesterase-influenced lipid metabolism during horse domestication.Cell reports · 2026Article
- Immunofunctions of Protein and Carbohydrate Assemblies Modulated by Structures Acrossing Scales as Biomaterials.Advanced materials (Deerfield Beach, Fla.) · 2026Review
- The Activity of Antimicrobial Peptides (AMPs) Identified Via an Integrated in Silico and Pilot in Vitro Screening Approach Towards ESKAPE Pathogens.Probiotics and antimicrobial proteins · 2026Article
- Development and evaluation of a multi-epitope subunit vaccine against Salmonella Enteritidis infection.Poultry science · 2026Article
- Genome-wide identification and expression analysis of chickpea U-box E3 ligases identifies CaPUB4 and CaPUB16 as candidate responsive genes for abiotic stress tolerance.Journal of applied genetics · 2026Article
- Applications and limitations of AI tools in enzyme design.Protein science : a publication of the Protein Society · 2026Review
- Immunoinformatics-driven multi-epitope vaccine design as a promising strategy against multidrug-resistant pathogens: a comprehensive review.Folia microbiologica · 2026Review
- Comprehensive genome-wide analysis of DUF668 gene family in potato reveals roles in growth and stress responses.Journal of applied genetics · 2026Article
- Structural and biochemical comparison of the FLVCR and CTL membrane protein families in eukaryotes.Life science alliance · 2026Article
- Immunoinformatics-based design of artificial chimeric proteins as universal vaccine candidates against foot-and-mouth disease virus serotypes A, O, and SAT2.Scientific reports · 2026Article
- Engineering molecularly imprinted polymers for receptor-specific cancer therapeutics.Nanoscale · 2026Review
- Structure of Crimean-Congo haemorrhagic fever virus RNA polymerase.Nature microbiology · 2026Article
- Structural insights into the Nipah virus nucleocapsid assembly.Communications biology · 2026Article
- Article
- Computational glycosyltransferases masked deoxynivalenol toxicity and halted FHB spread in wheat grains.Journal of advanced research · 2026Article
- Mimetics of in-cell and subcellular crowding and solvation for protein folding.Biochemical Society transactions · 2026Review
- Enzymatically controlled release of proteins and peptides: A promising, alternative secretion approach.iScience · 2026Article
286 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.