ArticleProceedings of the National Academy of Sciences of the United States of America2004
Automated structure prediction of weakly homologous proteins on a genomic scale.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 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
158 citing papers in PubMed.
- Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER.Nature biotechnology · 2026Article
- Chemosensory Receptors in Vertebrates: Structure and Computational Modeling Insights.International journal of molecular sciences · 2025Review
- The physics-AI dialogue in drug design.RSC medicinal chemistry · 2025Review
- An outlook on structural biology after AlphaFold: tools, limits and perspectives.FEBS open bio · 2025Review
- Uncovering the Interaction Interface Between Harpin (Hpa1) and Rice Aquaporin (OsPIP1;3) Through Protein-Protein Docking: An In Silico Approach.Molecular biotechnology · 2024Article
- Recent Progress of Protein Tertiary Structure Prediction.Molecules (Basel, Switzerland) · 2024Review
- De novo protein fold design through sequence-independent fragment assembly simulations.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- AI-driven pan-proteome analyses reveal insights into the biohydrometallurgical properties ofFrontiers in microbiology · 2023Article
- Deep learning geometrical potential for high-accuracyiScience · 2022Article
- Toward the solution of the protein structure prediction problem.The Journal of biological chemistry · 2021Review
- Deep learning techniques have significantly impacted protein structure prediction and protein design.Current opinion in structural biology · 2021Review
- A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction.PloS one · 2021Article
- Antimalarial Peptide and Polyketide Natural Products from the Fijian Marine CyanobacteriumMarine drugs · 2020Article
- I-TASSER gateway: A protein structure and function prediction server powered by XSEDE.Future generations computer systems : FGCS · 2019Article
- DESTINI: A deep-learning approach to contact-driven protein structure prediction.Scientific reports · 2019Article
- Selecting Near-Native Protein Structures from Predicted Decoy Sets Using Ordered Graphlet Degree Similarity.Genes · 2019Article
- Article
- Leishmania infantum 5'-Methylthioadenosine Phosphorylase presents relevant structural divergence to constitute a potential drug target.BMC structural biology · 2017Article
- Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.Molecules (Basel, Switzerland) · 2017Article
- 3D-QSAR and Molecular Docking Studies on the TcPMCA1-Mediated Detoxification of Scopoletin and Coumarin Derivatives.International journal of molecular sciences · 2017Article
98 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
2 authors.
Funding
Abstract
We have developed TASSER, a hierarchical approach to protein structure prediction that consists of template identification by threading, followed by tertiary structure assembly via the rearrangement of continuous template fragments guided by an optimized C(alpha) and side-chain-based potential driven by threading-based, predicted tertiary restraints. TASSER was applied to a comprehensive benchmark set of 1,489 medium-sized proteins in the Protein Data Bank. With homologues excluded, in 927 cases, the templates identified by our threading algorithm PROSPECTOR_3 have a rms deviation from native <6.5 A with approximately 80% alignment coverage. After template reassembly, this number increases to 1,172. This shows significant and systematic improvement of the final models with respect to the initial template alignments. Furthermore, significant improvements in loop modeling are demonstrated. We then apply TASSER to the 1,360 medium-sized ORFs in the Escherichia coli genome; approximately 920 can be predicted with high accuracy based on confidence criteria established in the Protein Data Bank benchmark. These results from our unprecedented comprehensive folding benchmark on all protein categories provide a reliable basis for the application of TASSER to structural genomics, especially to proteins of low sequence identity to solved protein structures.
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.