ArticleProteins2018
Protein structure prediction using Rosetta in CASP12.
Article in Proteins, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Navigating the uncharted: AI-driven advances in protein structure, dynamics, interactions and ligand interactions for understudied families.BioData mining · 2026Review
- Elucidating the link between NS-SNP-Induced protein conformational changes and drug resistance in Klebsiella pneumoniae.Archives of microbiology · 2026Article
- Antifungal Potential ofJournal of fungi (Basel, Switzerland) · 2026Article
- Protein Structure Prediction Methods.Advances in experimental medicine and biology · 2026Review
- ΦX174 bacteriophage viability predicted by protein biophysical modeling.bioRxiv : the preprint server for biology · 2025Article
- The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design.bioRxiv : the preprint server for biology · 2025Article
- Prediction of protein structural changes mediated by NS-SNPs in antibiotic resistance determinants in Streptococcus pneumoniae.Archives of microbiology · 2025Article
- In Silico Identification of Novel Compounds as Anthelmintics AgainstAnimals : an open access journal from MDPI · 2025Article
- Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.Journal of chemical theory and computation · 2024Article
- FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe.Genome biology · 2024Article
- iBio-GATS-A Semi-Automated Workflow for Structural Modelling of Insect Odorant Receptors.International journal of molecular sciences · 2024Article
- DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.Bioinformatics (Oxford, England) · 2023Article
- Immunoinformatics Strategy to Develop a Novel Universal Multiple Epitope-Based COVID-19 Vaccine.Vaccines · 2023Article
- Ab Initio Modelling of the Structure of ToxA-like and MAX Fungal Effector Proteins.International journal of molecular sciences · 2023Article
- Mechanistic Insight into the Suppression of Polyglutamine Aggregation by SRCP1.ACS chemical biology · 2023Article
- A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution.Frontiers in bioinformatics · 2023Article
- Protein Function Analysis through Machine Learning.Biomolecules · 2022Review
- Modeling SARS-CoV-2 proteins in the CASP-commons experiment.Proteins · 2021Article
- DATA-DRIVEN LEARNING OF GEOMETRIC SCATTERING MODULES FOR GNNS.IEEE International Workshop on Machine Learning for Signal Processing : [proceedings]. IEEE International Workshop on Machine Learning for Signal Processing · 2021Article
- Deep learning techniques have significantly impacted protein structure prediction and protein design.Current opinion in structural biology · 2021Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We describe several notable aspects of our structure predictions using Rosetta in CASP12 in the free modeling (FM) and refinement (TR) categories. First, we had previously generated (and published) models for most large protein families lacking experimentally determined structures using Rosetta guided by co-evolution based contact predictions, and for several targets these models proved better starting points for comparative modeling than any known crystal structure-our model database thus starts to fulfill one of the goals of the original protein structure initiative. Second, while our "human" group simply submitted ROBETTA models for most targets, for six targets expert intervention improved predictions considerably; the largest improvement was for T0886 where we correctly parsed two discontinuous domains guided by predicted contact maps to accurately identify a structural homolog of the same fold. Third, Rosetta all atom refinement followed by MD simulations led to consistent but small improvements when starting models were close to the native structure, and larger but less consistent improvements when starting models were further away.
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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.