Results 41 to 50 of about 254,467 (221)

GOPET: A tool for automated predictions of Gene Ontology terms

BMC Bioinformatics, 2006
Background Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task.
Glatting Karl-Heinz, Eils Roland, Schubert Falk, del Val Coral, Vinayagam Arunachalam, Suhai Sándor, König Rainer   +6 more
doaj   +1 more source

Function‐driven design of a surrogate interleukin‐2 receptor ligand

FEBS Letters, EarlyView.
Interleukin (IL)‐2 signaling can be achieved and precisely fine‐tuned through the affinity, distance, and orientation of the heterodimeric receptors with their ligands. We designed a biased IL‐2 surrogate ligand that selectively promotes effector T and natural killer cell activation and differentiation. Interleukin (IL) receptors play a pivotal role in
Ziwei Tang, Zelin Cheng, Teng Li, Fulian Wang, Liangminghui Zhang, Xiuxiu He, Lili Liu, Wei Wang, Aibin Liang, Guang Yang   +9 more
wiley   +1 more source

Improvements in viral gene annotation using large language models and soft alignments

BMC Bioinformatics
Background The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known proteins when using alignment, k-mer, or ...
William L. Harrigan, Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson, Zachary D. Schreiber, Mahdi Belcaid   +5 more
doaj   +1 more source

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

BMC Genomics, 2020
Background The process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-seq or mass spectrometry.
Michal Levin, Marion Scheibe, Falk Butter   +2 more
doaj   +1 more source

The newfound relationship between extrachromosomal DNAs and excised signal circles

FEBS Letters, EarlyView.
Extrachromosomal DNAs (ecDNAs) contribute to the progression of many human cancers. In addition, circular DNA by‐products of V(D)J recombination, excised signal circles (ESCs), have roles in cancer progression but have largely been overlooked. In this Review, we explore the roles of ecDNAs and ESCs in cancer development, and highlight why these ...
Dylan Casey, Zeqian Gao, Joan Boyes
wiley   +1 more source

Draft genome sequence of Venturia carpophila, the causal agent of peach scab

Standards in Genomic Sciences, 2017
Venturia carpophila causes peach scab, a disease that renders peach (Prunus persica) fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V.
Chunxian Chen, Clive H. Bock, Bruce W. Wood   +2 more
doaj   +1 more source

Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities. [PDF]

PLoS ONE, 2010
High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome.
Eric Venner, Andreas Martin Lisewski, Serkan Erdin, R Matthew Ward, Shivas R Amin, Olivier Lichtarge   +5 more
doaj   +1 more source

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

Structural instability impairs function of the UDP‐xylose synthase 1 Ile181Asn variant associated with short‐stature genetic syndrome in humans

FEBS Letters, EarlyView.
The Ile181Asn variant of human UDP‐xylose synthase (hUXS1), associated with a short‐stature genetic syndrome, has previously been reported as inactive. Our findings demonstrate that Ile181Asn‐hUXS1 retains catalytic activity similar to the wild‐type but exhibits reduced stability, a looser oligomeric state, and an increased tendency to precipitate ...
Tuo Li, Pedro A. Sánchez‐Murcia, Bernd Nidetzky   +2 more
wiley   +1 more source

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

BMC Bioinformatics, 2008
Background Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions.
Chen Brian Y, Erdin Serkan, Lisewski Andreas, Ward R Matthew, Kristensen David M, Fofanov Viacheslav Y, Kimmel Marek, Kavraki Lydia E, Lichtarge Olivier   +8 more
doaj   +1 more source