Results 81 to 90 of about 1,386,749 (339)

JPred4: a protein secondary structure prediction server

Nucleic Acids Res., 2015
JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction.
Alexey Drozdetskiy, C. Cole, J. Procter, G. Barton   +3 more
semanticscholar   +1 more source

Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation

FEBS Letters, EarlyView.
Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe, Tanmay Kumar Mohanty, Rashna Bhandari, Dorothea Fiedler   +3 more
wiley   +1 more source

Substrate specificity of Burkholderia pseudomallei multidrug transporters is influenced by the hydrophilic patch in the substrate‐binding pocket

FEBS Letters, EarlyView.
Multidrug transporters BpeB and BpeF from the Gram‐negative pathogen Burkholderia pseudomallei have a hydrophilic patch in their substrate‐binding pocket. Drug susceptibility tests and growth curve analyses using an Escherichia coli recombinant expression system revealed that the hydrophilic patches of BpeB and BpeF are involved in the substrate ...
Ui Okada, Satoshi Murakami
wiley   +1 more source

Time after time – circadian clocks through the lens of oscillator theory

FEBS Letters, EarlyView.
Oscillator theory bridges physics and circadian biology. Damped oscillators require external drivers, while limit cycles emerge from delayed feedback and nonlinearities. Coupling enables tissue‐level coherence, and entrainment aligns internal clocks with environmental cues.
Marta del Olmo, Carolin Ector, Hanspeter Herzel   +2 more
wiley   +1 more source

Prediction of protein-destabilizing polymorphisms by manual curation with protein structure. [PDF]

PLoS ONE, 2012
The relationship between sequence polymorphisms and human disease has been studied mostly in terms of effects of single nucleotide polymorphisms (SNPs) leading to single amino acid substitutions that change protein structure and function.
Craig Alan Gough, Keiichi Homma, Yumi Yamaguchi-Kabata, Makoto K Shimada, Ranajit Chakraborty, Yasuyuki Fujii, Hisakazu Iwama, Shinsei Minoshima, Shigetaka Sakamoto, Yoshiharu Sato, Yoshiyuki Suzuki, Masahito Tada-Umezaki, Ken Nishikawa, Tadashi Imanishi, Takashi Gojobori   +14 more
doaj   +1 more source

Water in protein structure prediction [PDF]

Proceedings of the National Academy of Sciences, 2004
Proteins have evolved to use water to help guide folding. A physically motivated, nonpairwise-additive model of water-mediated interactions added to a protein structure prediction Hamiltonian yields marked improvement in the quality of structure prediction for larger proteins.
Papoian, G A, Ulander, J, Eastwood, M P, Luthey-Schulten, Z, Wolynes, P G   +4 more
openaire   +3 more sources

The newfound relationship between extrachromosomal DNAs and excised signal circles

FEBS Letters, EarlyView.
Extrachromosomal DNAs (ecDNAs) contribute to the progression of many human cancers. In addition, circular DNA by‐products of V(D)J recombination, excised signal circles (ESCs), have roles in cancer progression but have largely been overlooked. In this Review, we explore the roles of ecDNAs and ESCs in cancer development, and highlight why these ...
Dylan Casey, Zeqian Gao, Joan Boyes
wiley   +1 more source

In situ molecular organization and heterogeneity of the Legionella Dot/Icm T4SS

FEBS Letters, EarlyView.
We present a nearly complete in situ model of the Legionella Dot/Icm type IV secretion system, revealing its central secretion channel and identifying new components. Using cryo‐electron tomography with AI‐based modeling, our work highlights the structure, variability, and mechanism of this complex nanomachine, advancing understanding of bacterial ...
Przemysław Dutka, Yuxi Liu, Stefano Maggi, Debnath Ghosal, Jue Wang, Prashant P. Damke, Stephen D. Carter, Wei Zhao, Sukhithasri Vijayrajratnam, Joseph P. Vogel, Carrie L. Shaffer, Grant J. Jensen   +11 more
wiley   +1 more source

Integration of Multi-Feature Fusion and PLS-DA in Protein Secondary Structure Prediction

MATEC Web of Conferences, 2016
Protein structure prediction has become one of the central problems in the field of modern computational biology. Protein secondary structure prediction is the basis of the spatial structure prediction of proteins.
Huang Guangzao, Tang Meishuang, Guan Jinting, Zhou Sun, Zhu Wenbing, Ji Guoli   +5 more
doaj   +1 more source

Hohai Graphic Protein Data Bank and Prediction Model [PDF]

Jisuanji kexue
Protein is a kind of substance with spatial structure.The main goal of protein structure prediction is to extract effective information from existing large-scale protein datasets,so as to predict the structure of proteins in nature.At present,one of the ...
WEI Xiangxiang, MENG Zhaohui
doaj   +1 more source