Structure‐based systems biology: a zoom lens for the cell

Aloy, Patrick; Russell, Robert B.

doi:10.1016/j.febslet.2005.02.014

Cited by 28 publications

(18 citation statements)

References 40 publications

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“…For example, we should mention the parallel array organization of fibroblasts and cardiomyocytes in native myocardial tissue that ensures adequate electrical properties or the alignment of collagen fibers in the bone that provides high tensile strength [177,178]. Therefore, tissue engineering strategies include the control of cellular alignment, which can be achieved by means of micropatterning techniques [179].…”

Section: Applications Of Poly(alkylene Dicarboxylate)smentioning

confidence: 99%

Synthesis, Properties and Applications of Biodegradable Polymers Derived from Diols and Dicarboxylic Acids: From Polyesters to Poly(ester amide)s

Díaz

Katsarava

Puiggalı́

2014

IJMS

209

112

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Poly(alkylene dicarboxylate)s constitute a family of biodegradable polymers with increasing interest for both commodity and speciality applications. Most of these polymers can be prepared from biobased diols and dicarboxylic acids such as 1,4-butanediol, succinic acid and carbohydrates. This review provides a current status report concerning synthesis, biodegradation and applications of a series of polymers that cover a wide range of properties, namely, materials from elastomeric to rigid characteristics that are suitable for applications such as hydrogels, soft tissue engineering, drug delivery systems and liquid crystals. Finally, the incorporation of aromatic units and α-amino acids is considered since stiffness of molecular chains and intermolecular interactions can be drastically changed. In fact, poly(ester amide)s derived from naturally occurring amino acids offer great possibilities as biodegradable materials for biomedical applications which are also extensively discussed.

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Section: Applications Of Poly(alkylene Dicarboxylate)smentioning

confidence: 99%

Synthesis, Properties and Applications of Biodegradable Polymers Derived from Diols and Dicarboxylic Acids: From Polyesters to Poly(ester amide)s

Díaz

Katsarava

Puiggalı́

2014

IJMS

209

112

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“…For success, systems biology must bridge engineering, mathematics, metabolism, molecular biology, and cell biology (49). The emerging field of free radical and redox biology should be at the foundation of this approach.…”

Section: The Redoxome In Systems Biologymentioning

confidence: 99%

Quantitative Redox Biology: An Approach to Understand the Role of Reactive Species in Defining the Cellular Redox Environment

Buettner

Wagner

Rodgers

2011

Cell Biochem Biophys

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Systems biology is now recognized as a needed approach to understand the dynamics of inter- and intra-cellular processes. Redox processes are at the foundation of nearly all aspects of biology. Free radicals, related oxidants, and antioxidants are central to the basic functioning of cells and tissues. They set the cellular redox environment and therefore are key to regulation of biochemical pathways and networks, thereby influencing organism health. To understand how short-lived, quasi-stable species, such as superoxide, hydrogen peroxide, and nitric oxide, connect to the metabolome, proteome, lipidome, and genome we need absolute quantitative information on all redox active compounds as well as thermodynamic and kinetic information on their reactions, i.e. knowledge of the complete redoxome. Central to the state of the redoxome are the interactive details of the superoxide/peroxide formation and removal systems. Quantitative information is essential to establish the dynamic mathematical models needed to reveal the temporal evolution of biochemical pathways and networks. This new field of Quantitative Redox Biology will allow researchers to identify new targets for intervention to advance our efforts to achieve optimal human health.

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“…For computational hotspot detection, most of the methods require knowledge of the protein-protein complex [2], [3], [10]. Likewise, structural knowledge of protein-protein complexes is valuable for understanding the complex connection between individual molecules and cell behavior [11]. Compared to the case of single protein structures, the number of experimentally determined structures of protein-protein complexes is still very limited.…”

Section: Introductionmentioning

confidence: 99%

DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking

et al. 2014

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The distance-dependent knowledge-based DrugScorePPI potentials, previously developed for in silico alanine scanning and hot spot prediction on given structures of protein-protein complexes, are evaluated as a scoring and objective function for the structure prediction of protein-protein complexes. When applied for ranking “unbound perturbation” (“unbound docking”) decoys generated by Baker and coworkers a 4-fold (1.5-fold) enrichment of acceptable docking solutions in the top ranks compared to a random selection is found. When applied as an objective function in FRODOCK for bound protein-protein docking on 97 complexes of the ZDOCK benchmark 3.0, DrugScorePPI/FRODOCK finds up to 10% (15%) more high accuracy solutions in the top 1 (top 10) predictions than the original FRODOCK implementation. When used as an objective function for global unbound protein-protein docking, fair docking success rates are obtained, which improve by ∼2-fold to 18% (58%) for an at least acceptable solution in the top 10 (top 100) predictions when performing knowledge-driven unbound docking. This suggests that DrugScorePPI balances well several different types of interactions important for protein-protein recognition. The results are discussed in view of the influence of crystal packing and the type of protein-protein complex docked. Finally, a simple criterion is provided with which to estimate a priori if unbound docking with DrugScorePPI/FRODOCK will be successful.

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Structure‐based systems biology: a zoom lens for the cell

Cited by 28 publications

References 40 publications

Synthesis, Properties and Applications of Biodegradable Polymers Derived from Diols and Dicarboxylic Acids: From Polyesters to Poly(ester amide)s

Synthesis, Properties and Applications of Biodegradable Polymers Derived from Diols and Dicarboxylic Acids: From Polyesters to Poly(ester amide)s

Quantitative Redox Biology: An Approach to Understand the Role of Reactive Species in Defining the Cellular Redox Environment

DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking

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