Results 31 to 40 of about 1,896,722 (263)

Progressive search in tandem mass spectrometry

BMC Bioinformatics, 2023
Background High-throughput Proteomics has been accelerated by (tandem) mass spectrometry. However, the slow speed of mass spectra analysis prevents the analysis results from being up-to-date.
Yoonsung Joh, Kangbae Lee, Hyunwoo Kim, Heejin Park   +3 more
doaj   +1 more source

Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events

Frontiers in Bioinformatics, 2023
Protein annotation errors can have significant consequences in a wide range of fields, ranging from protein structure and function prediction to biomedical research, drug discovery, and biotechnology.
Arnaud Kress, Olivier Poch, Odile Lecompte, Julie D. Thompson   +3 more
doaj   +1 more source

AlignScape, displaying sequence similarity using self-organizing maps

Frontiers in Bioinformatics
The current richness of sequence data needs efficient methodologies to display and analyze the complexity of the information in a compact and readable manner.
Isaac Filella-Merce, Isaac Filella-Merce, Vincent Mallet, Eric Durand, Michael Nilges, Guillaume Bouvier, Riccardo Pellarin, Riccardo Pellarin   +7 more
doaj   +1 more source

iSeqSearch: incremental protein search for iBlast/iMMSeqs2/iDiamond [PDF]

PeerJ
Background The advancement of sequencing technology has led to a rapid increase in the amount of DNA and protein sequence data; consequently, the size of genomic and proteomic databases is constantly growing.
Hyunwoo Yoo, Mohammadsaleh Refahi, Robi Polikar, Bahrad A. Sokhansanj, James R. Brown, Gail L. Rosen   +5 more
doaj   +2 more sources

BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Biology Direct, 2022
Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes ...
Markus Sutter, Cheryl A. Kerfeld
doaj   +1 more source

Computational curation and analysis of publicly available protein sequence data from a single protein family

MethodsX, 2022
The wealth of sequence data available on public databases is increasing at an exponential rate, and while tremendous efforts are being made to make access to these resources easier, these data can be challenging for researchers to reuse because ...
Kyra Dougherty, Katalin A. Hudak
doaj   +1 more source

PhosHSGN: Deep Neural Networks Combining Sequence and Protein Spatial Information to Improve Protein Phosphorylation Site Prediction

IEEE Access
Phosphorylation site prediction is one of the key processes in protein post-transcriptional modification. It is an important research direction in the field of bioinformatics and is of great significance for understanding protein function and signal ...
Jiale Lu, Haibin Chen, Ji Qiu
doaj   +1 more source

Filtering Degenerate Patterns with Application to Protein Sequence Analysis

Algorithms, 2013
In biology, the notion of degenerate pattern plays a central role for describing various phenomena. For example, protein active site patterns, like those contained in the PROSITE database, e.g., [FY ]DPC[LIM][ASG]C[ASG], are, in general, represented by ...
Matteo Comin, Davide Verzotto
doaj   +1 more source

Genomic landscape of drug binding and pharmacogenetic variation across diverse populations using SNPdrug3D

Nature Communications
One of the promises of precision medicine is to understand and act on inter-individual genetic differences in drug responses. SNPdrug3D contains the complete genomic landscape of missense single nucleotide variants (SNV) across the human proteome and at ...
Ashar J. Malik, Dimitar Kenanov, Cheng-Shoong Chong, Mert Burak Ozturk, Qiqi Wang, Hong-Yun Chang, Maxime Hebrard, Ying Swan Ho, Zhenxun Wang, Vachiranee Limviphuvadh, Jhoann M. T. Miyajima, Srinivasaraghavan Kannan, Roberto Tirado Magallanes, Xueling Sim, Jin Fang Chai, Sonia Davila, Khung Keong Yeo, Khai Pang Leong, Liuh Ling Goh, Neerja Karnani, Johan Gunnar Eriksson, Ching-Yu Cheng, Tien Yin Wong, Marie Loh, Rinkoo Dalan, Chiea Chuen Khor, Guo-Liang Chew, Weng Khong Lim, Joanne Ngeow, John C. Chambers, E. Shyong Tai, Nicolas Bertin, Chris Soon Heng Tan, Judice Koh, Patrick Tan, SG10K_Health Consortium, Chandra S. Verma, Sebastian Maurer-Stroh   +37 more
doaj   +1 more source

Personalized Zebrafish Models for Fusion‐Positive Pediatric Sarcomas

Pediatric Blood &Cancer, EarlyView.
ABSTRACT Clinical sequencing efforts have revolutionized our approaches to categorizing pediatric cancers in real time. This has dramatically improved our ability to profile pediatric tumors, identify actionable vulnerabilities, and influence clinical care.
Lisa H. Hall, Emma N. Harrison, Genevieve C. Kendall   +2 more
wiley   +1 more source