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 ◽  
...  
2019 ◽  
Author(s):  
Amaurys Ibarra ◽  
Gail J. Bartlett ◽  
Zsofia Hegedus ◽  
Som Dutt ◽  
Fruzsina Hobor ◽  
...  

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.


2014 ◽  
Vol 131 ◽  
pp. 16-21 ◽  
Author(s):  
Ling Ye ◽  
Qifan Kuang ◽  
Lin Jiang ◽  
Jiesi Luo ◽  
Yanping Jiang ◽  
...  

2014 ◽  
Vol 20 (8) ◽  
pp. 1192-1200 ◽  
Author(s):  
Jing Chen ◽  
Xiaomin Ma ◽  
Yaxia Yuan ◽  
Jianfeng Pei ◽  
Luhua Lai

2019 ◽  
Author(s):  
Amaurys Ibarra ◽  
Gail J. Bartlett ◽  
Zsofia Hegedus ◽  
Som Dutt ◽  
Fruzsina Hobor ◽  
...  

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.


Author(s):  
Pandjassarame Kangueane ◽  
Christina Nilofer
Keyword(s):  

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Yanhua Qiao ◽  
Yi Xiong ◽  
Hongyun Gao ◽  
Xiaolei Zhu ◽  
Peng Chen

2007 ◽  
Vol 68 (4) ◽  
pp. 803-812 ◽  
Author(s):  
Irina S. Moreira ◽  
Pedro A. Fernandes ◽  
Maria J. Ramos

2011 ◽  
Vol 52 (1) ◽  
pp. 120-133 ◽  
Author(s):  
Alexander Metz ◽  
Christopher Pfleger ◽  
Hannes Kopitz ◽  
Stefania Pfeiffer-Marek ◽  
Karl-Heinz Baringhaus ◽  
...  

2020 ◽  
Vol 8 (6) ◽  
pp. 1308-1312

Crimes Hot spots are areas that have a greater than average number of criminal or disorder events. Recently, many researchers pay more attentions for detecting crime hot spots to allow police personnel to plan effectively for emergency response, determine mitigation priorities, analyze historical events, and predict future events. This paper introduces a fuzzy geographical model for detecting crimes hot spots. The proposed model has three main phases which are: (1) Pre-processing, (2) Fuzzification, and (3) Visualization. In pre-processing phase, the model uses statistical methods and cleansing techniques to clean the raw dataset. In Fuzzification phase, the number of crimes converts into linguistic value according to the hybrid (triangular and trapezoidal) membership function. In visualization phase, the results are visualized on GIS map with different colors based on the density of crime hot spot. This paper aims to rank the hotspot crime places in the country, so the decision-makers can be knowing accurately. Our dataset collected from Cairo crimes at year 2016 and the results of our approach suitable and has a good manner for the decision maker with high accuracy.


2013 ◽  
Vol 135 (16) ◽  
pp. 6242-6256 ◽  
Author(s):  
Mary S. Golden ◽  
Shaun M. Cote ◽  
Marianna Sayeg ◽  
Brandon S. Zerbe ◽  
Elizabeth A. Villar ◽  
...  

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