Results 81 to 90 of about 2,642,890 (372)

Fourier Analysis of Conservation Patterns in Protein Secondary Structure

Computational and Structural Biotechnology Journal, 2017
Residue conservation is a common observation in alignments of protein families, underscoring positions important in protein structure and function. Though many methods measure the level of conservation of particular residue positions, currently we do not
Ashok Palaniappan, Eric Jakobsson
doaj   +1 more source

Protein Secondary Structure Detection in Intermediate Resolution Cryo-EM Maps Using Deep Learning

Nature Methods, 2019
Although structures determined at near-atomic resolution are now routinely reported by cryo-electron microscopy (cryo-EM), many density maps are determined at an intermediate resolution, and extracting structure information from these maps is still a ...
Sai R Maddhuri Venkata Subramaniya, Genki Terashi, D. Kihara   +2 more
semanticscholar   +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

Two State Behavior in a Solvable Model of $\beta$-hairpin folding

, 1999
Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $\beta$-hairpin, motivated by the fact that folding of a $\beta$-hairpin ...
A. Finkelstein, A. Kilonski, A. R. Dinner, Chinlin Guo, D. Cule, D. K. Klimov, David A. Kessler, Herbert Levine, J. N. Onuchic, K. A. Dill, P. G. Wolynes, R. Du, S-J. Chen, S. Takada, T. Dauxois, T. Dauxois, V. Muñoz, V. Muñoz, V. S. Pande, V. S. Pande   +19 more
core   +1 more source

A novel method for comparing topological models of protein structures enhanced with ligand information [PDF]

, 2008
This article is available open access through the publisher’s website through the link below. Copyright @ 2008 The Authors.We introduce TOPS+ strings, a highly abstract string-based model of protein topology that permits efficient computation of ...
Gilbert, D, Veeramalai, M
core   +1 more source

Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction

Scientific Reports, 2019
Protein Secondary Structure prediction has been a central topic of research in Bioinformatics for decades. In spite of this, even the most sophisticated ab initio SS predictors are not able to reach the theoretical limit of three-state prediction ...
Mirko Torrisi, Manaz Kaleel, G. Pollastri   +2 more
semanticscholar   +1 more source

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields [PDF]

Scientific Reports, 2015
Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been ...
Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu   +3 more
semanticscholar   +1 more source

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

Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks

Bioinform., 2018
Motivation Sequence-based prediction of one dimensional structural properties of proteins has been a long-standing subproblem of protein structure prediction.
Jack Hanson, K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou   +4 more
semanticscholar   +1 more source

Sequence determinants of RNA G‐quadruplex unfolding by Arg‐rich regions

FEBS Letters, EarlyView.
We show that Arg‐rich peptides selectively unfold RNA G‐quadruplexes, but not RNA stem‐loops or DNA/RNA duplexes. This length‐dependent activity is inhibited by acidic residues and is conserved among SR and SR‐related proteins (SRSF1, SRSF3, SRSF9, U1‐70K, and U2AF1).
Naiduwadura Ivon Upekala De Silva, Puspa Kunwar, Md Ibnul Rifat Rahman, Joanna Koryo Kwao, Nathan Lehman, Zihan Zhang, Trenton Paul, Claire Cheng, Nicholas Truex, Hui‐Ting Lee, Jun Zhang   +10 more
wiley   +1 more source