ArticlePloS one2011
Generalized fragment picking in Rosetta: design, protocols and applications.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
102 citing papers in PubMed.
- Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling.Journal of chemical theory and computation · 2026Article
- Exploring the structural lexicon of the Proteome via Metric Geometry.PLoS computational biology · 2026Article
- A Review of Current Computational Tools for Peptide-Protein Docking.Journal of computational chemistry · 2026Review
- Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling.bioRxiv : the preprint server for biology · 2026Article
- Sortase-mediated ligation of cytochrome c peroxidase and cytochrome c highlights the roles of dynamics and conformational specificity for interprotein electron transfer.Journal of inorganic biochemistry · 2026Article
- Morpheus: a fragment-based algorithm to predict fold-switching behaviour in proteins across proteomes.Bioinformatics (Oxford, England) · 2025Article
- Deep learning-guided design of dynamic proteins.Science (New York, N.Y.) · 2025Article
- Enzyme Engineering: Performance Optimization, Novel Sources, and Applications in the Food Industry.Foods (Basel, Switzerland) · 2024Review
- Sparks of function by de novo protein design.Nature biotechnology · 2024Review
- Current Computational Methods for Protein-peptide Complex Structure Prediction.Current medicinal chemistry · 2024Review
- Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.Briefings in bioinformatics · 2023Article
- Construction of Histone-Protein Complex Structures by Peptide Growing.International journal of molecular sciences · 2023Article
- Elucidation of Short Linear Motif-Based Interactions of the FERM Domains of Ezrin, Radixin, Moesin, and Merlin.Biochemistry · 2023Article
- Sparse pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction.Journal of biomolecular NMR · 2023Article
- Sequence-structure-function relationships in the microbial protein universe.Nature communications · 2023Article
- PROFASA-a web-based protein fragment and structure analysis workstation.Frontiers in bioengineering and biotechnology · 2023Article
- Low-resolution description of the conformational space for intrinsically disordered proteins.Scientific reports · 2022Article
- Protein Design: From the Aspect of Water Solubility and Stability.Chemical reviews · 2022Review
- Targeted Mutagenesis of the MulticopyPlants (Basel, Switzerland) · 2022Article
- Multi-level analysis of intrinsically disordered protein docking methods.Methods (San Diego, Calif.) · 2022Article
42 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The Rosetta de novo structure prediction and loop modeling protocols begin with coarse grained Monte Carlo searches in which the moves are based on short fragments extracted from a database of known structures. Here we describe a new object oriented program for picking fragments that greatly extends the functionality of the previous program (nnmake) and opens the door for new approaches to structure modeling. We provide a detailed description of the code design and architecture, highlighting its modularity, and new features such as extensibility, total control over the fragment picking workflow and scoring system customization. We demonstrate that the program provides at least as good building blocks for ab-initio structure prediction as the previous program, and provide examples of the wide range of applications that are now accessible.
Indexed as
Identifiers
What OpenQuestion holds
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.