BioMed Research International

Network Proteomics: From Protein Structure to Protein-Protein Interaction


Status
Published

Lead Editor

1Soochow University, Suzhou, China

2University of Campus Bio-Medico, Rome, Italy

3University of Pittsburgh, Pittsburgh, USA

4Oak Ridge National Laboratory, Oak Ridge, USA


Network Proteomics: From Protein Structure to Protein-Protein Interaction

Description

With the emergence of high-throughput “omics” data, network theory is being increasingly used to analyze biomolecular systems. Combined with traditional computational methods, such as molecular dynamics (MD) simulation and normal mode analysis (NMA), the representation of proteins as amino acid networks provides an effective method to quantitatively investigate protein structures through network descriptors, as well as studying allosterism in proteins in terms of pathway analysis. Accordingly, network languages decipher new information in the paradigm from structure to function. In fact, proteins, as the basic units for biological functions, rarely act alone, which prompted the arrival of proteomics. “Network proteomics” is just defined as the research area that introduce network theory to investigate biological networks ranging from protein structure networks to protein interaction networks, including protein-protein and protein-DNA/RNA interactions. This area lies somewhere between structural biology and systems biology, which can be rapidly moving towards full biological network analysis. In addition, the application of network proteomics in biomedical fields has increased significantly. For example, the study of allosteric sites and hotspots could help us to understand molecular mechanisms of various diseases, as well as providing putative new therapeutic targets.

This special issue intends to collect contributions, not only focusing on the state of the art of methodology in “network proteomics” itself, but also focusing on the current status and future direction of their applications in translational medical informatics.

Potential topics include, but are not limited to:

  • Advances in amino acid network (or protein contact network, protein structure network, and residue interaction network)
  • Elastic network model for proteins
  • Dynamic network analysis for proteins
  • Protein-protein interaction network and disease
  • Biological networks analysis (i.e., transcriptional networks and metabolic networks)
  • Network-based drug design
  • Network biomarkers in proteomics

Articles

  • Special Issue
  • - Volume 2017
  • - Article ID 8929613
  • - Editorial

Network Proteomics: From Protein Structure to Protein-Protein Interaction

Guang Hu | Luisa Di Paola | ... | Intawat Nookaew
  • Special Issue
  • - Volume 2017
  • - Article ID 3572394
  • - Research Article

Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists

Yuwei Wang | Rui Han | ... | Paola Gramatica
  • Special Issue
  • - Volume 2017
  • - Article ID 2483264
  • - Review Article

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

Guang Hu | Luisa Di Paola | ... | Alessandro Giuliani
  • Special Issue
  • - Volume 2016
  • - Article ID 8518945
  • - Review Article

Biomolecular Network-Based Synergistic Drug Combination Discovery

Xiangyi Li | Guangrong Qin | ... | Lu Xie
  • Special Issue
  • - Volume 2016
  • - Article ID 4354901
  • - Research Article

Identification of Hot Spots in Protein Structures Using Gaussian Network Model and Gaussian Naive Bayes

Hua Zhang | Tao Jiang | Guogen Shan
  • Special Issue
  • - Volume 2016
  • - Article ID 7086390
  • - Research Article

Identification of Novel Inhibitors against Coactivator Associated Arginine Methyltransferase 1 Based on Virtual Screening and Biological Assays

Fei Ye | Weiyao Zhang | ... | Cheng Luo
  • Special Issue
  • - Volume 2016
  • - Article ID 8036450
  • - Research Article

Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

Hua Wan | Shan Chang | ... | Mei-hua Wang
  • Special Issue
  • - Volume 2016
  • - Article ID 9795409
  • - Research Article

Networks Models of Actin Dynamics during Spermatozoa Postejaculatory Life: A Comparison among Human-Made and Text Mining-Based Models

Nicola Bernabò | Alessandra Ordinelli | ... | Barbara Barboni
  • Special Issue
  • - Volume 2016
  • - Article ID 2509385
  • - Research Article

Comparison of FDA Approved Kinase Targets to Clinical Trial Ones: Insights from Their System Profiles and Drug-Target Interaction Networks

Jingyu Xu | Panpan Wang | ... | Feng Zhu
  • Special Issue
  • - Volume 2016
  • - Article ID 8124636
  • - Research Article

Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study

Nachon Raethong | Jirasak Wong-ekkabut | ... | Wanwipa Vongsangnak
BioMed Research International
 Journal metrics
Acceptance rate30%
Submission to final decision66 days
Acceptance to publication35 days
CiteScore3.600
Impact Factor2.276
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