Building alternate protein structures using the elastic network model

2009 ◽  
Vol 74 (3) ◽  
pp. 682-700 ◽  
Author(s):  
Qingyi Yang ◽  
Kim A. Sharp
Keyword(s):  
Network Model ◽  
Protein Structures ◽  
Elastic Network Model ◽  
Elastic Network

scholarly journals Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case

2017 ◽  
Vol 2017 ◽  
pp. 1-15 ◽  
Author(s):  
Guang Hu ◽  
Luisa Di Paola ◽  
Zhongjie Liang ◽  
Alessandro Giuliani
Keyword(s):  
Comparative Study ◽  
Network Model ◽  
Protein Complexes ◽  
Protein Structures ◽  
Contact Network ◽  
Elastic Network Model ◽  
Elastic Network ◽  
Protein Contact Network ◽  
Structural Systems Biology ◽  
Allosteric Mechanisms

The overall topology and interfacial interactions play key roles in understanding structural and functional principles of protein complexes. Elastic Network Model (ENM) and Protein Contact Network (PCN) are two widely used methods for high throughput investigation of structures and interactions within protein complexes. In this work, the comparative analysis of ENM and PCN relative to hemoglobin (Hb) was taken as case study. We examine four types of structural and dynamical paradigms, namely, conformational change between different states of Hbs, modular analysis, allosteric mechanisms studies, and interface characterization of an Hb. The comparative study shows that ENM has an advantage in studying dynamical properties and protein-protein interfaces, while PCN is better for describing protein structures quantitatively both from local and from global levels. We suggest that the integration of ENM and PCN would give a potential but powerful tool in structural systems biology.

scholarly journals Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

2016 ◽  
Vol 145 (1) ◽  
pp. 014104 ◽  
Author(s):  
Chunhua Li ◽  
Dashuai Lv ◽  
Lei Zhang ◽  
Feng Yang ◽  
Cunxin Wang ◽  
...  
Keyword(s):  
Network Model ◽  
Coarse Grained ◽  
Elastic Network Model ◽  
Elastic Network ◽  
Folding Dynamics

scholarly journals Generalization of the elastic network model for the study of large conformational changes in biomolecules

2018 ◽  
Vol 20 (25) ◽  
pp. 17020-17028 ◽  
Author(s):  
Adolfo B. Poma ◽  
Mai Suan Li ◽  
Panagiotis E. Theodorakis
Keyword(s):  
Network Model ◽  
Conformational Changes ◽  
Elastic Network Model ◽  
Elastic Network

The generalized elastic network (GEN) model enables the study of large conformational changes in proteins.

A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes

2019 ◽  
Vol 21 (8) ◽  
pp. 4359-4366 ◽  
Author(s):  
D. Vijay Anand ◽  
Zhenyu Meng ◽  
Kelin Xia
Keyword(s):  
Normal Mode ◽  
Network Model ◽  
Material Properties ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Particle Model ◽  
Elastic Network Model ◽  
Elastic Network ◽  
Virtual Particle ◽  
Biomolecular Complexes

The CMVP-ENM for virus normal mode analysis. With a special ratio parameter, CMVP-ENM can characterize the multi-material properties of biomolecular complexes and systematically enhance or suppress the modes for different components.

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