Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors

Bioinformatics ◽

10.1093/bioinformatics/btr657 ◽

2011 ◽

Vol 28 (3) ◽

pp. 331-341 ◽

Author(s):

Ke Chen ◽

Marcin J. Mizianty ◽

Lukasz Kurgan

Keyword(s):

Nucleotide Binding ◽

Structural Descriptors ◽

Binding Residues

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Identification of protein-nucleotide binding residues via graph regularized k-local hyperplane distance nearest neighbor model

Applied Intelligence ◽

10.1007/s10489-021-02737-0 ◽

2021 ◽

Author(s):

Yijie Ding ◽

Chao Yang ◽

Jijun Tang ◽

Fei Guo

Keyword(s):

Nearest Neighbor ◽

Nucleotide Binding ◽

Binding Residues ◽

Local Hyperplane

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Accurate prediction of ATP-binding residues using sequence and sequence-derived structural descriptors

2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) ◽

10.1109/bibm.2010.5706533 ◽

2010 ◽

Author(s):

Ke Chen ◽

J. Mizianty Marcin ◽

Lukasz Kurgan

Keyword(s):

Accurate Prediction ◽

Atp Binding ◽

Structural Descriptors ◽

Binding Residues

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Guanine Nucleotide-Binding Protein G(I)/G(S)/G(T) Subunit Beta-2

10.32388/xmibnr ◽

2020 ◽

Author(s):

Keyword(s):

Binding Protein ◽

Nucleotide Binding ◽

Protein G ◽

Guanine Nucleotide ◽

Guanine Nucleotide Binding Protein ◽

Beta 2 ◽

Guanine Nucleotide Binding ◽

Nucleotide Binding Protein

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Novel mutation in X-linked inhibitor of apoptosis (XIAP) in two Chinese Singapore brothers with nucleotide-binding and oligomerisation domain (NOD)-2 signalling defect

10.26226/morressier.594a7d46d462b8028d89355a ◽

2017 ◽

Author(s):

Zhong Youjia

Keyword(s):

Novel Mutation ◽

Nucleotide Binding ◽

Inhibitor Of Apoptosis

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Faculty Opinions recommendation of Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1006433.372966 ◽

2006 ◽

Author(s):

Edward Egelman

Keyword(s):

Binding Site ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Terminal Domain

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Faculty Opinions recommendation of Nucleotide binding to human uncoupling protein-2 refolded from bacterial inclusion bodies.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1006648.82706 ◽

2002 ◽

Author(s):

Daniel Ricquier

Keyword(s):

Inclusion Bodies ◽

Uncoupling Protein ◽

Nucleotide Binding ◽

Uncoupling Protein 2

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Faculty Opinions recommendation of Projection structure of P-glycoprotein by electron microscopy. Evidence for a closed conformation of the nucleotide binding domains.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1009972.140509 ◽

2002 ◽

Author(s):

Wil Konings

Keyword(s):

Electron Microscopy ◽

Nucleotide Binding ◽

Closed Conformation ◽

Binding Domains ◽

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Faculty Opinions recommendation of Unusual nucleotide-binding properties of the chloroplast protein import receptor, atToc33.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1014228.193161 ◽

2003 ◽

Author(s):

Steven Theg

Keyword(s):

Protein Import ◽

Nucleotide Binding ◽

Binding Properties ◽

Chloroplast Protein Import ◽

Chloroplast Protein ◽

Import Receptor

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Faculty Opinions recommendation of The C-terminal domain of the nucleotide-binding domain protein Wzt determines substrate specificity in the ATP-binding cassette transporter for the lipopolysaccharide O-antigens in Escherichia coli serotypes O8 and O9a.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1027346.328490 ◽

2005 ◽

Author(s):

Miguel Valvano

Keyword(s):

Escherichia Coli ◽

Substrate Specificity ◽

Nucleotide Binding ◽

Binding Domain ◽

Atp Binding ◽

Nucleotide Binding Domain ◽

Terminal Domain ◽

Atp Binding Cassette Transporter ◽

Domain Protein ◽

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An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

Protein and Peptide Letters ◽

10.2174/0929866527666200625202028 ◽

2020 ◽

Vol 27 ◽

Author(s):

Fırat Kurt

Keyword(s):

Stress Responses ◽

Chelating Agent ◽

Biological Processes ◽

Biotic And Abiotic Stress ◽

Oligopeptide Transporter ◽

Binding Residues ◽

Fe Homeostasis ◽

Proteins Interactions ◽

Insight Into ◽

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

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