scholarly journals Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-κB Essential Modulator/IKKβ Protein–Protein Interface

2013 ◽  
Vol 135 (16) ◽  
pp. 6242-6256 ◽  
Author(s):  
Mary S. Golden ◽  
Shaun M. Cote ◽  
Marianna Sayeg ◽  
Brandon S. Zerbe ◽  
Elizabeth A. Villar ◽  
...  
Keyword(s):  
Binding Energy ◽  
Hot Spots ◽  
Computational Analysis ◽  
Protein Interface ◽  
Analysis Of Binding Energy

scholarly journals POSITRONIUM DECAY: GAUGE INVARIANCE AND ANALYTICITY

2002 ◽  
Vol 17 (10) ◽  
pp. 1355-1398 ◽  
Author(s):  
J. PESTIEAU ◽  
C. SMITH ◽  
S. TRINE
Keyword(s):  
Wave Function ◽  
Form Factor ◽  
Binding Energy ◽  
Gauge Invariance ◽  
Dispersion Relations ◽  
Decay Rates ◽  
Effective Form ◽  
Theoretical Predictions ◽  
Positronium Decay ◽  
Analysis Of Binding Energy

The construction of positronium decay amplitudes is handled through the use of dispersion relations. In this way, emphasis is put on basic QED principles: gauge invariance and soft-photon limits (analyticity).A firm grounding is given to the factorization approaches, and some ambiguities in the spin and energy structures of the positronium wave function are removed. Nonfactorizable amplitudes are naturally introduced. Their dynamics are described, especially regarding the enforcement of gauge invariance and analyticity through delicate interferences. The important question of the completeness of the present theoretical predictions for the decay rates is then addressed. Indeed, some of those nonfactorizable contributions are unaccounted for by NRQED analyses. However, it is shown that such new contributions are highly suppressed, being of [Formula: see text].Finally, a particular effective form factor formalism is constructed for parapositronium, allowing a thorough analysis of binding energy effects and analyticity implementation.

scholarly journals Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces

2019 ◽  
Author(s):  
Amaurys Ibarra ◽  
Gail J. Bartlett ◽  
Zsofia Hegedus ◽  
Som Dutt ◽  
Fruzsina Hobor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Comparative Analysis ◽  
Hot Spots ◽  
Hot Spot ◽  
Accurate Prediction ◽  
Protein Interface ◽  
Alanine Scanning ◽  
Protein Interfaces ◽  
Structural Ensembles ◽  
Α Helix

Here we describe a comparative analysis of multiple CAS methods, which highlights effective approaches to improve the accuracy of predicting hot-spot residues. Alongside this, we introduce a new method, BUDE Alanine Scanning, which can be applied to single structures from crystallography, and to structural ensembles from NMR or molecular dynamics data. The comparative analyses facilitate accurate prediction of hot-spots that we validate experimentally with three diverse targets: NOXA-B/MCL-1 (an α helix-mediated PPI), SIMS/SUMO and GKAP/SHANK-PDZ (both β strand-mediated interactions). Finally, the approach is applied to the accurate prediction of hot-residues at a topographically novel Affimer/BCL-xL protein-protein interface.

scholarly journals RELATIVISTIC MEAN FIELD STUDY OF ISLANDS OF INVERSION IN NEUTRON-RICH Z = 17–23, 37–40 AND 60–64 NUCLEI

2013 ◽  
Vol 22 (04) ◽  
pp. 1350018 ◽  
Author(s):  
S. K. SINGH ◽  
S. MAHAPATRO ◽  
R. N. MISHRA
Keyword(s):  
Binding Energy ◽  
Periodic Table ◽  
Mean Field ◽  
Quadrupole Deformation ◽  
Neutron Separation Energy ◽  
Mean Square ◽  
Separation Energy ◽  
Relativistic Mean Field ◽  
Field Formalism ◽  
Analysis Of Binding Energy

We study the extremely neutron-rich nuclei for Z = 17–23, 37–40 and 60–64 regions of the periodic table by using axially deformed relativistic mean field formalism with NL3* parametrization. Based on the analysis of binding energy, two neutron separation energy, quadrupole deformation and root mean square radii, we emphasized the speciality of these considered regions which are recently predicted islands of inversion.

Prediction of hot spots residues in protein–protein interface using network feature and microenvironment feature

2014 ◽  
Vol 131 ◽  
pp. 16-21 ◽  
Author(s):  
Ling Ye ◽  
Qifan Kuang ◽  
Lin Jiang ◽  
Jiesi Luo ◽  
Yanping Jiang ◽  
...  
Keyword(s):  
Hot Spots ◽  
Protein Interface ◽  
Network Feature

Protein-Protein Interface Analysis and Hot Spots Identification for Chemical Ligand Design

2014 ◽  
Vol 20 (8) ◽  
pp. 1192-1200 ◽  
Author(s):  
Jing Chen ◽  
Xiaomin Ma ◽  
Yaxia Yuan ◽  
Jianfeng Pei ◽  
Luhua Lai
Keyword(s):  
Hot Spots ◽  
Ligand Design ◽  
Protein Interface ◽  
Interface Analysis

scholarly journals Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein–Protein Interaction in Solution and Determination of Binding Energy Hot Spots

Biochemistry ◽  
2015 ◽  
Vol 54 (40) ◽  
pp. 6162-6175 ◽  
Author(s):  
Yan Wang ◽  
Huili Yao ◽  
Yuan Cheng ◽  
Scott Lovell ◽  
Kevin P. Battaile ◽  
...  
Keyword(s):  
Binding Energy ◽  
Protein Interaction ◽  
Hot Spots ◽  
Protein Protein Interaction

scholarly journals SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Irina S. Moreira ◽  
Panagiotis I. Koukos ◽  
Rita Melo ◽  
Jose G. Almeida ◽  
Antonio J. Preto ◽  
...  
Keyword(s):  
Hot Spots ◽  
High Accuracy ◽  
Protein Interface

scholarly journals Computational analysis by molecular docking of thirty alkaloid compounds from medicinal plants as potent inhibitors of SARS-CoV-2 main protease

2021 ◽  
Vol 4 (4) ◽  
pp. 487-503
Author(s):  
Tunga Kuhana A ◽  
◽  
Jason T. Kilembe ◽  
Aristote Matondo ◽  
Khamis M. Yussuf ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Medicinal Plants ◽  
Computational Analysis ◽  
Potential Drug ◽  
Lipinski’S Rule ◽  
Main Protease ◽  
Lipinski’S Rule Of Five ◽  
Potential Inhibitors ◽  
Therapeutic Profile

Year 2020 has been highly affected by the COVID-19 outbreak. The urgent need for a potent and effective drug for the treatment of this malignancy put pressure on researchers and scientists worldwide to develop a potential drug or a vaccine to resist SARS-CoV-2 virus. We report in this paper the assessment of the efficiency of thirty alkaloid compounds derived from African medicinal plants against the SARS-CoV-2 main protease through molecular docking and bioinformatics approaches. The results revealed four potential inhibitors (ligands 18, 21, 23 and 24) with 12.26 kcal/mol being the highest binding energy. Additionally, in silico drug-likeness and ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) properties for the four ligands showed a good predicted therapeutic profile of druggability, and fully obey the Lipinski's rule of five as well.

scholarly journals Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces

2019 ◽  
Author(s):  
Amaurys Ibarra ◽  
Gail J. Bartlett ◽  
Zsofia Hegedus ◽  
Som Dutt ◽  
Fruzsina Hobor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Comparative Analysis ◽  
Hot Spots ◽  
Hot Spot ◽  
Accurate Prediction ◽  
Protein Interface ◽  
Alanine Scanning ◽  
Protein Interfaces ◽  
Structural Ensembles ◽  
Α Helix

Here we describe a comparative analysis of multiple CAS methods, which highlights effective approaches to improve the accuracy of predicting hot-spot residues. Alongside this, we introduce a new method, BUDE Alanine Scanning, which can be applied to single structures from crystallography, and to structural ensembles from NMR or molecular dynamics data. The comparative analyses facilitate accurate prediction of hot-spots that we validate experimentally with three diverse targets: NOXA-B/MCL-1 (an α helix-mediated PPI), SIMS/SUMO and GKAP/SHANK-PDZ (both β strand-mediated interactions). Finally, the approach is applied to the accurate prediction of hot-residues at a topographically novel Affimer/BCL-xL protein-protein interface.

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