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Challenges in structural approaches to cell modeling.

Title: Challenges in structural approaches to cell modeling.
Name(s): Im, Wonpil, author
Liang, Jie, author
Olson, Arthur, author
Zhou, Huan-Xiang, author
Vajda, Sandor, author
Vakser, Ilya A, author
Type of Resource: text
Genre: Journal Article
Date Issued: 2016-07-31
Physical Form: computer
online resource
Extent: 1 online resource
Language(s): English
Abstract/Description: Computational modeling is essential for structural characterization of biomolecular mechanisms across the broad spectrum of scales. Adequate understanding of biomolecular mechanisms inherently involves our ability to model them. Structural modeling of individual biomolecules and their interactions has been rapidly progressing. However, in terms of the broader picture, the focus is shifting toward larger systems, up to the level of a cell. Such modeling involves a more dynamic and realistic representation of the interactomes in vivo, in a crowded cellular environment, as well as membranes and membrane proteins, and other cellular components. Structural modeling of a cell complements computational approaches to cellular mechanisms based on differential equations, graph models, and other techniques to model biological networks, imaging data, etc. Structural modeling along with other computational and experimental approaches will provide a fundamental understanding of life at the molecular level and lead to important applications to biology and medicine. A cross section of diverse approaches presented in this review illustrates the developing shift from the structural modeling of individual molecules to that of cell biology. Studies in several related areas are covered: biological networks; automated construction of three-dimensional cell models using experimental data; modeling of protein complexes; prediction of non-specific and transient protein interactions; thermodynamic and kinetic effects of crowding; cellular membrane modeling; and modeling of chromosomes. The review presents an expert opinion on the current state-of-the-art in these various aspects of structural modeling in cellular biology, and the prospects of future developments in this emerging field.
Identifier: FSU_pmch_27255863 (IID), 10.1016/j.jmb.2016.05.024 (DOI), PMC4976022 (PMCID), 27255863 (RID), 27255863 (EID), S0022-2836(16)30193-0 (PII)
Keywords: Cellular membranes, Chromosome modeling, Macromolecular crowding, Modeling of biological mesoscale, Protein interactions
Grant Number: R01 GM092950, R01 GM088187, R01 GM074255, R01 GM093147, R35 GM118078, R01 GM079804, R01 GM061867, U54 GM087519, P41 GM103426
Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at
Subject(s): Cell Membrane/ultrastructure
Computational Biology/methods
Computer Simulation
Membrane Proteins/metabolism
Models, Biological
Models, Molecular
Persistent Link to This Record:
Host Institution: FSU
Is Part Of: Journal of molecular biology.
Issue: iss. 15, vol. 428

Choose the citation style.
Im, W., Liang, J., Olson, A., Zhou, H. -X., Vajda, S., & Vakser, I. A. (2016). Challenges in structural approaches to cell modeling. Journal Of Molecular Biology. Retrieved from