Advanced Protein Alignments Based on Sequence, Structure and Hydropathy Profiles; The Paradigm of the Viral Polymerase Enzyme
Sign Up to like & getrecommendations! Published in 2017 at "Mathematics in Computer Science"
DOI: 10.1007/s11786-016-0287-8
Abstract: One of the major drawbacks of modern bioinformatics is the fact that protein similarity and blast searches are still based on primary amino acid sequence rather than structural data. Primary sequence searches are inadequate, as… read more here.
Keywords: protein; alignments based; sequence structure; hydropathy ... See more keywords
Sequence and structure-based peptides as potent amyloid inhibitors: A review.
Sign Up to like & getrecommendations! Published in 2020 at "Archives of biochemistry and biophysics"
DOI: 10.1016/j.abb.2020.108614
Abstract: Misfolded and natively disordered globular proteins tend to aggregate together in an interwoven fashion to form fibrous, proteinaceous deposits referred to as amyloid fibrils. Formation and deposition of such insoluble fibrils are the characteristic features… read more here.
Keywords: peptides potent; structure based; sequence structure; structure ... See more keywords
18S rRNA gene sequence-structure phylogeny of the Trypanosomatida (Kinetoplastea, Euglenozoa) with special reference to Trypanosoma.
Sign Up to like & getrecommendations! Published in 2021 at "European journal of protistology"
DOI: 10.1016/j.ejop.2021.125824
Abstract: Parasites of the order Trypanosomatida are known due to their medical relevance. Despite the progress made in the past decades on understanding the evolution of this group of organisms, there are still many open questions… read more here.
Keywords: 18s rrna; sequence structure; rrna gene;
Sequence- and structure-based computational analyses of Gram-negative tripartite efflux pumps in the context of bacterial membranes.
Sign Up to like & getrecommendations! Published in 2018 at "Research in microbiology"
DOI: 10.1016/j.resmic.2018.01.002
Abstract: Gram-negative multidrug resistance currently presents a serious threat to public health with infections effectively rendered untreatable. Multiple molecular mechanisms exist that cause antibiotic resistance and in addition, the last three decades have seen slowing rates… read more here.
Keywords: gram negative; negative tripartite; resistance; sequence structure ... See more keywords
Highly Similar Sequence and Structure Yet Different Biophysical Behavior: A Computational Study of Two Triosephosphate Isomerases
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.1c01501
Abstract: Homodimeric triosephosphate isomerases (TIMs) from Trypanosoma cruzi (TcTIM) and Trypanosoma brucei (TbTIM) have markedly similar amino-acid sequences and three-dimensional structures. However, several of their biophysical parameters, such as their susceptibility to sulfhydryl agents and their… read more here.
Keywords: highly similar; sequence structure; triosephosphate isomerases; triosephosphate ... See more keywords
Insights of Life Molecules' Dynamic Distribution in Live Cells via Sequence-Structure Bispecific Fluorescent RNA.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.3c03626
Abstract: Life molecules' distributions in live systems construct the complex dynamic reaction networks, whereas it is still challenging to demonstrate the dynamic distributions of biomolecules in live systems. Herein, we proposed a dynamic analysis strategy via… read more here.
Keywords: structure; rna; life molecules; structure bispecific ... See more keywords
Structural facets of POU2F1 in light of the functional annotations and sequence-structure patterns
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Biomolecular Structure and Dynamics"
DOI: 10.1080/07391102.2020.1733092
Abstract: Abstract POU domain class 2 homebox 1 or POU2F1 is broadly known as an important transcription factor. Due to its association with different types of malignancies, POU2F1 became one of the key factors in pancancer… read more here.
Keywords: structural facets; facets pou2f1; sequence structure; structure ... See more keywords
A comparative study of sequence- and structure-based features of small RNAs and other RNAs of bacteria
Sign Up to like & getrecommendations! Published in 2018 at "RNA Biology"
DOI: 10.1080/15476286.2017.1387709
Abstract: ABSTRACT Small RNAs (sRNAs) in bacteria have emerged as key players in transcriptional and post-transcriptional regulation of gene expression. Here, we present a statistical analysis of different sequence- and structure-related features of bacterial sRNAs to… read more here.
Keywords: comparative study; small rnas; study sequence; sequence structure ... See more keywords
Sequence-structure relations of biopolymers.
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw621
Abstract: Motivation DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as structural semantics… read more here.
Keywords: information; structure relations; sequence structure; structure ... See more keywords
MolArt: a molecular structure annotation and visualization tool
Sign Up to like & getrecommendations! Published in 2018 at "Bioinformatics"
DOI: 10.1093/bioinformatics/bty489
Abstract: Abstract Summary MolArt fills the gap between sequence and structure visualization by providing a light-weight, interactive environment enabling exploration of sequence annotations in the context of available experimental or predicted protein structures. Provided a UniProt… read more here.
Keywords: sequence annotations; molart; visualization; sequence structure ... See more keywords
Sequence-to-structure dependence of isolated IgG Fc complex biantennary N-glycans: a molecular dynamics study
Sign Up to like & getrecommendations! Published in 2019 at "Glycobiology"
DOI: 10.1093/glycob/cwy097
Abstract: Fc glycosylation of human immunoglobulins G (IgGs) is essential for their structural integrity and activity. Interestingly, the specific nature of the Fc glycoforms is known to modulate the IgG effector function and inflammatory properties. Indeed,… read more here.
Keywords: igg; molecular dynamics; complex biantennary; sequence structure ... See more keywords