scholarly journals RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database

2016 ◽  
Vol 44 (W1) ◽  
pp. W562-W567 ◽  
Author(s):  
Zhichao Miao ◽  
Eric Westhof
Keyword(s):  
Nucleic Acid ◽  
Large Scale ◽  
Web Server ◽  
Nucleic Acid Binding ◽  
Binding Residues ◽  
High Level

scholarly journals GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues

2021 ◽  
Author(s):  
Ying Xia ◽  
Chun-Qiu Xia ◽  
Xiaoyong Pan ◽  
Hong-Bin Shen
Keyword(s):  
Neural Networks ◽  
Nucleic Acid ◽  
Biological Activities ◽  
New Drugs ◽  
Superior Performance ◽  
Nucleic Acid Binding ◽  
Hierarchical Graph ◽  
Binding Residue ◽  
Binding Residues ◽  
Graph Neural Networks

Abstract Knowledge of the interactions between proteins and nucleic acids is the basis of understanding various biological activities and designing new drugs. How to accurately identify the nucleic-acid-binding residues remains a challenging task. In this paper, we propose an accurate predictor, GraphBind, for identifying nucleic-acid-binding residues on proteins based on an end-to-end graph neural network. Considering that binding sites often behave in highly conservative patterns on local tertiary structures, we first construct graphs based on the structural contexts of target residues and their spatial neighborhood. Then, hierarchical graph neural networks (HGNNs) are used to embed the latent local patterns of structural and bio-physicochemical characteristics for binding residue recognition. We comprehensively evaluate GraphBind on DNA/RNA benchmark datasets. The results demonstrate the superior performance of GraphBind than state-of-the-art methods. Moreover, GraphBind is extended to other ligand-binding residue prediction to verify its generalization capability. Web server of GraphBind is freely available at http://www.csbio.sjtu.edu.cn/bioinf/GraphBind/.

Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains

2017 ◽  
Vol 20 (4) ◽  
pp. 1250-1268 ◽  
Author(s):  
Jian Zhang ◽  
Zhiqiang Ma ◽  
Lukasz Kurgan
Keyword(s):  
Nucleic Acid ◽  
Ligand Binding ◽  
Protein Binding ◽  
Large Scale ◽  
Rna Binding ◽  
Solvent Accessibility ◽  
Residue Level ◽  
Relative Solvent Accessibility ◽  
Data Set ◽  
Binding Residues

Abstract Proteins interact with a variety of molecules including proteins and nucleic acids. We review a comprehensive collection of over 50 studies that analyze and/or predict these interactions. While majority of these studies address either solely protein–DNA or protein–RNA binding, only a few have a wider scope that covers both protein–protein and protein–nucleic acid binding. Our analysis reveals that binding residues are typically characterized with three hallmarks: relative solvent accessibility (RSA), evolutionary conservation and propensity of amino acids (AAs) for binding. Motivated by drawbacks of the prior studies, we perform a large-scale analysis to quantify and contrast the three hallmarks for residues that bind DNA-, RNA-, protein- and (for the first time) multi-ligand-binding residues that interact with DNA and proteins, and with RNA and proteins. Results generated on a well-annotated data set of over 23 000 proteins show that conservation of binding residues is higher for nucleic acid- than protein-binding residues. Multi-ligand-binding residues are more conserved and have higher RSA than single-ligand-binding residues. We empirically show that each hallmark discriminates between binding and nonbinding residues, even predicted RSA, and that combining them improves discriminatory power for each of the five types of interactions. Linear scoring functions that combine these hallmarks offer good predictive performance of residue-level propensity for binding and provide intuitive interpretation of predictions. Better understanding of these residue-level interactions will facilitate development of methods that accurately predict binding in the exponentially growing databases of protein sequences.

scholarly journals Identification of Nucleic Acid Binding Residues in the FCS Domain of the Polycomb Group Protein Polyhomeotic

Biochemistry ◽  
2011 ◽  
Vol 50 (22) ◽  
pp. 4998-5007 ◽  
Author(s):  
Renjing Wang ◽  
Udayar Ilangovan ◽  
Belinda Z. Leal ◽  
Angela K. Robinson ◽  
Barbara T. Amann ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Polycomb Group ◽  
Nucleic Acid Binding ◽  
Polycomb Group Protein ◽  
Group Protein ◽  
Binding Residues

scholarly journals SNBRFinder: A Sequence-Based Hybrid Algorithm for Enhanced Prediction of Nucleic Acid-Binding Residues

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0133260 ◽  
Author(s):  
Xiaoxia Yang ◽  
Jia Wang ◽  
Jun Sun ◽  
Rong Liu
Keyword(s):  
Nucleic Acid ◽  
Hybrid Algorithm ◽  
Nucleic Acid Binding ◽  
Binding Residues

Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

1992 ◽  
Vol 50 (1) ◽  
pp. 762-763
Author(s):  
Stephen D. Jett
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Carbon Coated ◽  
Nucleoprotein Complexes ◽  
Mobility Shift Assay ◽  
Protein Nucleic Acid ◽  
Gel Mobility Shift ◽  
Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

Social inequality in the evolution of human societies

2019 ◽  
pp. 98-120
Author(s):  
Georgi Derluguian
Keyword(s):  
Social Inequality ◽  
Large Scale ◽  
Human Beings ◽  
Mass Violence ◽  
Public And Private ◽  
Tangible Assets ◽  
Transition To Agriculture ◽  
New Institutions ◽  
High Level ◽  
Political Economic

The author develops ideas about the origin of social inequality during the evolution of human societies and reflects on the possibilities of its overcoming. What makes human beings different from other primates is a high level of egalitarianism and altruism, which contributed to more successful adaptability of human collectives at early stages of the development of society. The transition to agriculture, coupled with substantially increasing population density, was marked by the emergence and institutionalisation of social inequality based on the inequality of tangible assets and symbolic wealth. Then, new institutions of warfare came into existence, and they were aimed at conquering and enslaving the neighbours engaged in productive labour. While exercising control over nature, people also established and strengthened their power over other people. Chiefdom as a new type of polity came into being. Elementary forms of power (political, economic and ideological) served as a basis for the formation of early states. The societies in those states were characterised by social inequality and cruelties, including slavery, mass violence and numerous victims. Nowadays, the old elementary forms of power that are inherent in personalistic chiefdom are still functioning along with modern institutions of public and private bureaucracy. This constitutes the key contradiction of our time, which is the juxtaposition of individual despotic power and public infrastructural one. However, society is evolving towards an ever more efficient combination of social initiatives with the sustainability and viability of large-scale organisations.

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