ArticleGene2008
BCL::Align-sequence alignment and fold recognition with a custom scoring function online.
Article in Gene, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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Who cites it
11 citing papers in PubMed.
- Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors.PloS one · 2021Article
- The homology model of PMP22 suggests mutations resulting in peripheral neuropathy disrupt transmembrane helix packing.Biochemistry · 2014Article
- Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions.Journal of computer-aided molecular design · 2013Article
- Article
- Virtual interactomics of proteins from biochemical standpoint.Molecular biology international · 2012Article
- CONTSOR--a new knowledge-based fold recognition potential, based on side chain orientation and contacts between residue terminal groups.Protein science : a publication of the Protein Society · 2012Article
- Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking.Proteins · 2010Article
- 3PFDB--a database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach.BioData mining · 2009Article
- The Kir channel immunoglobulin domain is essential for Kir1.1 (ROMK) thermodynamic stability, trafficking and gating.Channels (Austin, Tex.)Article
- Unique gating properties of C. elegans ClC anion channel splice variants are determined by altered CBS domain conformation and the R-helix linker.Channels (Austin, Tex.)Article
- Improved prediction of trans-membrane spans in proteins using an Artificial Neural Network.IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology proceedings. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational BiologyArticle
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
bcl:Align is a multiple sequence alignment tool that utilizes the dynamic programming method in combination with a customizable scoring function for sequence alignment and fold recognition. The scoring function is a weighted sum of the traditional PAM and BLOSUM scoring matrices, position-specific scoring matrices output by PSI-BLAST, secondary structure predicted by a variety of methods, chemical properties, and gap penalties. By adjusting the weights, the method can be tailored for fold recognition or sequence alignment tasks at different levels of sequence identity. A Monte Carlo algorithm was used to determine optimized weight sets for sequence alignment and fold recognition that most accurately reproduced the SABmark reference alignment test set. In an evaluation of sequence alignment performance, BCL::Align ranked best in alignment accuracy (Cline score of 22.90 for sequences in the Twilight Zone) when compared with Align-m, ClustalW, T-Coffee, and MUSCLE. ROC curve analysis indicates BCL::Align's ability to correctly recognize protein folds with over 80% accuracy. The flexibility of the program allows it to be optimized for specific classes of proteins (e.g. membrane proteins) or fold families (e.g. TIM-barrel proteins). BCL::Align is free for academic use and available online at http://www.meilerlab.org/.
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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.