ArticleScientific reports2016
ProQ3: Improved model quality assessments using Rosetta energy terms.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Efficient global accuracy estimation for protein complex structural models using multi-view representation learning.Cell reports methods · 2026Article
- DeepUMQA-X: Comprehensive and insightful estimation of model accuracy for protein single-chain and complex.Nucleic acids research · 2025Article
- $\mathcal{S}$ able: bridging the gap in protein structure understanding with an empowering and versatile pre-training paradigm.Briefings in bioinformatics · 2025Article
- Physical-aware model accuracy estimation for protein complex using deep learning method.Computational and structural biotechnology journal · 2025Article
- Bioinformatic Analysis of WNT Family Proteins.Bioinformatics and biology insights · 2025Article
- Recent advances and challenges in protein complex model accuracy estimation.Computational and structural biotechnology journal · 2024Review
- NEKL-4 regulates microtubule stability and mitochondrial health in ciliated neurons.The Journal of cell biology · 2024Article
- Protein structure accuracy estimation using geometry-complete perceptron networks.Protein science : a publication of the Protein Society · 2024Article
- NEKL-4 regulates microtubule stability and mitochondrial health inbioRxiv : the preprint server for biology · 2024Article
- Assessing protein model quality based on deep graph coupled networks using protein language model.Briefings in bioinformatics · 2023Article
- Deep Learning for Genomics: From Early Neural Nets to Modern Large Language Models.International journal of molecular sciences · 2023Review
- Article
- An In Silico Bioremediation Study to Identify Essential Residues of Metallothionein Enhancing the Bioaccumulation of Heavy Metals inMicroorganisms · 2023Article
- A gated graph transformer for protein complex structure quality assessment and its performance in CASP15.Bioinformatics (Oxford, England) · 2023Article
- Protein quality assessment with a loss function designed for high-quality decoys.Frontiers in bioinformatics · 2023Article
- Contact-Assisted Threading in Low-Homology Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A combinedCell cycle (Georgetown, Tex.) · 2022Article
- Article
- Using steered molecular dynamic tension for assessing quality of computational protein structure models.Journal of computational chemistry · 2022Article
- DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network.BMC bioinformatics · 2022Article
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4 authors.
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Abstract
Quality assessment of protein models using no other information than the structure of the model itself has been shown to be useful for structure prediction. Here, we introduce two novel methods, ProQRosFA and ProQRosCen, inspired by the state-of-art method ProQ2, but using a completely different description of a protein model. ProQ2 uses contacts and other features calculated from a model, while the new predictors are based on Rosetta energies: ProQRosFA uses the full-atom energy function that takes into account all atoms, while ProQRosCen uses the coarse-grained centroid energy function. The two new predictors also include residue conservation and terms corresponding to the agreement of a model with predicted secondary structure and surface area, as in ProQ2. We show that the performance of these predictors is on par with ProQ2 and significantly better than all other model quality assessment programs. Furthermore, we show that combining the input features from all three predictors, the resulting predictor ProQ3 performs better than any of the individual methods. ProQ3, ProQRosFA and ProQRosCen are freely available both as a webserver and stand-alone programs at http://proq3.bioinfo.se/.
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