ArticleProceedings of the National Academy of Sciences of the United States of America2014
Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed.
- Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences.Proteins · 2024Article
- Rapid discrimination between deleterious and benign missense mutations in the CAGI 6 experiment.Human genomics · 2024Article
- Design and characterization of a protein fold switching network.Nature communications · 2023Article
- The dynamic basis of structural order in proteins.Proteins · 2022Article
- Dynamic and conformational switching in proteins.Biopolymers · 2021Article
- The structure of protein dynamic space.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Sequence-specific dynamic information in proteins.Proteins · 2019Article
- Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments.Molecules (Basel, Switzerland) · 2018Article
- A weighted string kernel for protein fold recognition.BMC bioinformatics · 2017Article
- Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Global informatics and physical property selection in protein sequences.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Nonlinearities in protein space limit the utility of informatics in protein biophysics.Proteins · 2015Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- Alternative approach to protein structure prediction based on sequential similarity of physical properties.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- 3D representations of amino acids-applications to protein sequence comparison and classification.Computational and structural biotechnology journal · 2014Article
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 show that a Fourier-based sequence distance function is able to identify structural homologs of target sequences with high accuracy. It is shown that Fourier distances correlate very strongly with independently determined structural distances between molecules, a property of the method that is not attainable using conventional representations. It is further shown that the ability of the Fourier approach to identify protein folds is statistically far in excess of random expectation. It is then shown that, in actual searches for structural homologs of selected target sequences, the Fourier approach gives excellent results. On the basis of these results, we suggest that the global information detected by the Fourier representation is an essential feature of structure encoding in protein sequences and a key to structural homology detection.
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.