Results 71 to 80 of about 756,544 (331)

Substrate specificity of Burkholderia pseudomallei multidrug transporters is influenced by the hydrophilic patch in the substrate‐binding pocket

FEBS Letters, EarlyView.
Multidrug transporters BpeB and BpeF from the Gram‐negative pathogen Burkholderia pseudomallei have a hydrophilic patch in their substrate‐binding pocket. Drug susceptibility tests and growth curve analyses using an Escherichia coli recombinant expression system revealed that the hydrophilic patches of BpeB and BpeF are involved in the substrate ...
Ui Okada, Satoshi Murakami
wiley   +1 more source

A statistical score for assessing the quality of multiple sequence alignments

BMC Bioinformatics, 2006
Background Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures, building phylogenetic trees etc.
Aittokallio Tero, Ahola Virpi, Vihinen Mauno, Uusipaikka Esa   +3 more
doaj   +1 more source

ProbCons: Probabilistic consistency-based multiple sequence alignment.

Genome Research, 2005
To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high ...
Chuong B. Do, Mahathi S. Mahabhashyam, M. Brudno, S. Batzoglou   +3 more
semanticscholar   +1 more source

Multiple ETS family transcription factors bind mutant p53 via distinct interaction regions

FEBS Letters, EarlyView.
Mutant p53 gain‐of‐function is thought to be mediated by interaction with other transcription factors. We identify multiple ETS transcription factors that can bind mutant p53 and found that this interaction can be promoted by a PXXPP motif. ETS proteins that strongly bound mutant p53 were upregulated in ovarian cancer compared to ETS proteins that ...
Stephanie A. Metcalf, Nicholas F. Downing, Kaitlyn M. Mills, Samuel C. Metcalfe, Alexander E. Kritzer, Lindsey D. Mayo, Peter C. Hollenhorst   +6 more
wiley   +1 more source

Sequence embedding for fast construction of guide trees for multiple sequence alignment

Algorithms for Molecular Biology, 2010
Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences.
Wilm Andreas, Shi Weifeng, Sievers Fabian, Blackshields Gordon, Higgins Desmond G   +4 more
doaj   +1 more source

Progressive multiple sequence alignments from triplets [PDF]

BMC Bioinformatics, 2007
The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors ...
Kruspe, Matthias, Stadler, Peter F.
openaire   +4 more sources

An upstream open reading frame regulates expression of the mitochondrial protein Slm35 and mitophagy flux

FEBS Letters, EarlyView.
This study reveals how the mitochondrial protein Slm35 is regulated in Saccharomyces cerevisiae. The authors identify stress‐responsive DNA elements and two upstream open reading frames (uORFs) in the 5′ untranslated region of SLM35. One uORF restricts translation, and its mutation increases Slm35 protein levels and mitophagy.
Hernán Romo‐Casanueva, Ariann E. Mendoza‐Martínez, P. Abril Medina‐Flores, Carlos Campero‐Basaldua, Alexander DeLuna, Soledad Funes   +5 more
wiley   +1 more source

Mauve: multiple alignment of conserved genomic sequence with rearrangements.

Genome Research, 2004
As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into ...
A. Darling, B. Mau, F. Blattner, N. Perna   +3 more
semanticscholar   +1 more source

In situ molecular organization and heterogeneity of the Legionella Dot/Icm T4SS

FEBS Letters, EarlyView.
We present a nearly complete in situ model of the Legionella Dot/Icm type IV secretion system, revealing its central secretion channel and identifying new components. Using cryo‐electron tomography with AI‐based modeling, our work highlights the structure, variability, and mechanism of this complex nanomachine, advancing understanding of bacterial ...
Przemysław Dutka, Yuxi Liu, Stefano Maggi, Debnath Ghosal, Jue Wang, Prashant P. Damke, Stephen D. Carter, Wei Zhao, Sukhithasri Vijayrajratnam, Joseph P. Vogel, Carrie L. Shaffer, Grant J. Jensen   +11 more
wiley   +1 more source

SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation

BMC Bioinformatics, 2011
Background Multiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields.
Strope Cory L, Anderson Catherine L, Moriyama Etsuko N   +2 more
doaj   +1 more source