Results 1 to 10 of about 443,532 (143)
Frontiers in Genetics, 2022 Background: Aortic dissection (AD) is a life-threatening disease. Chromatin regulators (CRs) are indispensable epigenetic regulators. We aimed to identify differentially expressed chromatin regulators (DECRs) for AD diagnosis.Methods: We downloaded the ...
Chunjiang Liu +6 more
doaj +1 more source
Adaptive Residue-wise Profile Fusion for Low Homologous Protein SecondaryStructure Prediction Using External Knowledge [PDF]
arXiv, 2021 Protein secondary structure prediction (PSSP) is essential for protein function analysis. However, for low homologous proteins, the PSSP suffers from insufficient input features. In this paper, we explicitly import external self-supervised knowledge for low homologous PSSP under the guidance of residue-wise profile fusion.
arxiv
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model [PDF]
PLoS Comput Biol 13(1): e1005324, 2017, 2016 Recently exciting progress has been made on protein contact prediction, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence ...
arxiv +1 more source
arXiv, 2023 While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three ...
arxiv
Fundamental constraints on the abundances of chemotaxis proteins [PDF]
Biophys. J. 108(5): 1293-1305 (2015), 2015 Flagellated bacteria, such as Escherichia coli, perform directed motion in gradients of concentration of attractants and repellents in a process called chemotaxis. The E. coli chemotaxis signaling pathway is a model for signal transduction, but it has unique features.
arxiv +1 more source
FoldExplorer: Fast and Accurate Protein Structure Search with Sequence-Enhanced Graph Embedding [PDF]
arXiv, 2023 The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional alignment-based methods are dedicated to precise comparisons between pairs, exhibiting high accuracy. However, their
arxiv
A generative angular model of protein structure evolution [PDF]
Molecular Biology and Evolution, 34(8):2085-2100, 2017, 2016 Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a generative, evolutionary model of protein structure and sequence that is valid on a local length scale.
arxiv +1 more source
Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains [PDF]
PLoS Computational Biology, Public Library of Science, 2018, 14
(2), pp.e1006008, 2018 The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins.
arxiv +1 more source
Remote Homology Detection in Proteins Using Graphical Models [PDF]
, 2013 Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than sequence over long evolutionary distances, recognizing remote protein homologs from their sequence poses a challenge.
arxiv +1 more source