Simulation and analysis of in vitro DNA evolution [PDF]
, 2003 We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic simulations of ...
Chao Tang +6 more
core +1 more source
Organoids in pediatric cancer research
FEBS Letters, EarlyView.Organoid technology has revolutionized cancer research, yet its application in pediatric oncology remains limited. Recent advances have enabled the development of pediatric tumor organoids, offering new insights into disease biology, treatment response, and interactions with the tumor microenvironment.
Carla Ríos Arceo, Jarno Drost
wiley +1 more source
LPBERT: A Protein–Protein Interaction Prediction Method Based on a Pre-Trained Language Model
Applied SciencesThe prediction of protein–protein interactions is a key task in proteomics. Since protein sequences are easily available and understandable, they have become the primary data source for predicting protein–protein interactions.
An Hu, Linai Kuang, Dinghai Yang
doaj +1 more source
Molecules, 2018 Protein-protein interactions (PPIs) play important roles in various aspects of the structural and functional organization of cells; thus, detecting PPIs is one of the most important issues in current molecular biology.
Tao Wang +5 more
doaj +1 more source
Protein-Protein Interactions Prediction Based on Graph Energy and Protein Sequence Information
Molecules, 2020 Identification of protein-protein interactions (PPIs) plays an essential role in the understanding of protein functions and cellular biological activities. However, the traditional experiment-based methods are time-consuming and laborious.
Da Xu +4 more
doaj +1 more source
Transformer Neural Networks Attending to Both Sequence and Structure for Protein Prediction Tasks [PDF]
, 2022 Anowarul Kabir, Amarda Shehu
openalex +1 more source
FEBS Letters, EarlyView.Fluorescent probes allow dynamic visualization of phosphoinositides in living cells (left), whereas mass spectrometry provides high‐sensitivity, isomer‐resolved quantitation (right). Their synergistic use captures complementary aspects of lipid signaling. This review illustrates how these approaches reveal the spatiotemporal regulation and quantitative
Hiroaki Kajiho +3 more
wiley +1 more source
Discover protein sequence signatures from protein-protein interaction data
BMC Bioinformatics, 2005 Background The development of high-throughput technologies such as yeast two-hybrid systems and mass spectrometry technologies has made it possible to generate large protein-protein interaction (PPI) datasets.
Haasl Ryan J +3 more
doaj +1 more source
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. [PDF]
, 2014 BackgroundBacteroides spp. form a significant part of our gut microbiome and are well known for optimized metabolism of diverse polysaccharides. Initial analysis of the archetypal Bacteroides thetaiotaomicron genome identified 172 glycosyl hydrolases and
Axelrod, Herbert L +7 more
core +2 more sources
A Novel Scalable Apache Spark Based Feature Extraction Approaches for Huge Protein Sequence and their Clustering Performance Analysis [PDF]
, 2022 Preeti Jha +7 more
openalex +1 more source