Results 41 to 50 of about 113,363 (75)

Exploring hydrophilic sequence space to search for uncharted foldable proteins by AlphaFold2

Biophysics and Physicobiology
Proteins typically fold into unique three-dimensional structures largely driven by interactions between hydrophobic amino acids. This understanding has helped improve our knowledge of protein folding.
Naoki Tomita, Hiroki Onoda, Leonard M. G. Chavas, George Chikenji   +3 more
doaj   +1 more source

Complete Genome Sequence Analysis of a Dengue Case Co-Infected with Type I and Type II Imported into Jiaxing in 2023

Microbiology Research
In 2023, one case of coinfection with type I and type II dengue virus of imported origin was first reported in Jiaxing city. Therefore, we analysed the results of the molecular tracing analysis of this case.
Yamei Zhou, Shencong Lv, Hao Yan, Ganglin Ren, Yin Song, Jimei Jj, Lina Li, Yong Yan, Guoying Zhu   +8 more
doaj   +1 more source

Evidence of Divergent Amino Acid Usage in Comparative Analyses of R5- and X4-Associated HIV-1 Vpr Sequences

International Journal of Genomics, 2017
Vpr is an HIV-1 accessory protein that plays numerous roles during viral replication, and some of which are cell type dependent. To test the hypothesis that HIV-1 tropism extends beyond the envelope into the vpr gene, studies were performed to identify ...
Gregory C. Antell, Will Dampier, Benjamas Aiamkitsumrit, Michael R. Nonnemacher, Vanessa Pirrone, Wen Zhong, Katherine Kercher, Shendra Passic, Jean Williams, Yucheng Liu, Tony James, Jeffrey M. Jacobson, Zsofia Szep, Brian Wigdahl, Fred C. Krebs   +14 more
doaj   +1 more source

ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

BMC Bioinformatics, 2012
Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that ...
Meiler Arno, Klinger Claudia, Kaufmann Michael   +2 more
doaj   +1 more source

Amino acid substitution matrices for protein conformation identification [PDF]

arXiv, 2004
Methods for alignment of protein sequences typically measure similarity by using substitution matrix with scores for all possible exchanges of one amino acid with another. Although widely used, the matrices derived from homologous sequence segments, such as Dayhoff's PAM matrices and Henikoff's BLOSUM matrices, are not specific for protein conformation
arxiv  

Analysis of two duplications of the LDL receptor gene affectingintracellular transport, catabolism, and surface binding of the LDLreceptor

Journal of Lipid Research, 1998
Two novel mutations of the low density lipoprotein (LDL)-receptor genewere found in two Italian familial hypercholesterolemia (FH)-heterozygotes. Thefirst mutation was an 18 nucleotide duplication in exon 8 which is preceded byan A→T transversion.
Dilip.D. Patel, Nicoletta Lelli, Rita Garuti, Salvatore Li Volti, Stefano Bertolini, Brian L. Knight, Sebastiano Calandra   +6 more
doaj  

Coevolution-based inference of amino acid interactions underlying protein function

eLife, 2018
Protein function arises from a poorly understood pattern of energetic interactions between amino acid residues. Sequence-based strategies for deducing this pattern have been proposed, but lack of benchmark data has limited experimental verification. Here,
Victor H Salinas, Rama Ranganathan
doaj   +1 more source

Understanding conserved amino acids in proteins [PDF]

arXiv, 2000
It has been conjectured that evolution exerted pressure to preserve amino acids bearing thermodynamic, kinetic, and functional roles. In this letter we show that the physical requirement to maintain protein stability gives rise to a sequence conservatism pattern that is in remarkable agreement with that found in natural proteins.
arxiv  

Amino acid sequences of proteins from Leptospira serovar pomona

Memorias do Instituto Oswaldo Cruz, 2000
This report describes a partial amino acid sequences from three putative outer envelope proteins from Leptospira serovar pomona. In order to obtain internal fragments for protein sequencing, enzymatic and chemical digestion was performed.
Alves Selmo F, LeFebvre Rance B, Probert William   +2 more
doaj  

Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors

BMC Bioinformatics, 2010
Background Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices.
Zimmermann Karel, Gibrat Jean-François
doaj   +1 more source