ArticleBMC bioinformatics2014
Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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
6 citing papers in PubMed.
- CRFalign: A Sequence-Structure Alignment of Proteins Based on a Combination of HMM-HMM Comparison and Conditional Random Fields.Molecules (Basel, Switzerland) · 2022Article
- A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.BMC bioinformatics · 2016Article
- GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data.Frontiers in microbiology · 2016Article
- Article
- A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11.BMC bioinformatics · 2015Article
- An Improved Integration of Template-Based and Template-Free Protein Structure Modeling Methods and its Assessment in CASP11.Protein and peptide letters · 2015Article
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
backgroundProtein sequence profile-profile alignment is an important approach to recognizing remote homologs and generating accurate pairwise alignments. It plays an important role in protein sequence database search, protein structure prediction, protein function prediction, and phylogenetic analysis.
resultsIn this work, we integrate predicted solvent accessibility, torsion angles and evolutionary residue coupling information with the pairwise Hidden Markov Model (HMM) based profile alignment method to improve profile-profile alignments. The evaluation results demonstrate that adding predicted relative solvent accessibility and torsion angle information improves the accuracy of profile-profile alignments. The evolutionary residue coupling information is helpful in some cases, but its contribution to the improvement is not consistent.
conclusionIncorporating the new structural information such as predicted solvent accessibility and torsion angles into the profile-profile alignment is a useful way to improve pairwise profile-profile alignment methods.
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.