Searching for the Pareto frontier in multi-objective protein design

Nanda, Vikas; Belure, Sandeep V.; Shir, Ofer M.

doi:10.1007/s12551-017-0288-0

Cited by 6 publications

(3 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Multiobjective optimization algorithms have been applied to simultaneously promote the formation of the specific target association and disfavor the competing states, leading to the design of an abc heterotrimer capable of specific assembly (37) and an obligate abc heterotrimer where folding requires all three chains (18). However, the lack of high-resolution structural information critically limits our ability to control stability and specificity, particularly under conditions of increasing the complexity (38)(39)(40).…”

mentioning

confidence: 99%

How electrostatic networks modulate specificity and stability of collagen

Zheng

Lü

Lei

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.

show abstract

mentioning

confidence: 99%

How electrostatic networks modulate specificity and stability of collagen

Zheng

Lü

Lei

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

show abstract

“…1 and Additional file 1 : Figure S5. This can be drawn in parallel to “Pareto-distribution” that is eminent in across fields of natural sciences and economics [ 23 , 24 ]. The variance in protein space in “Prevalent” and “Non-prevalent” groups are majorly influenced by the nature of “structure class”.…”

Section: Resultsmentioning

confidence: 99%

ProLego: tool for extracting and visualizing topological modules in protein structures

2018

View full text Add to dashboard Cite

BackgroundIn protein design, correct use of topology is among the initial and most critical feature. Meticulous selection of backbone topology aids in drastically reducing the structure search space. With ProLego, we present a server application to explore the component aspect of protein structures and provide an intuitive and efficient way to scan the protein topology space.ResultWe have implemented in-house developed “topological representation” in an automated-pipeline to extract protein topology from given protein structure. Using the topology string, ProLego, compares topology against a non-redundant extensive topology database (ProLegoDB) as well as extracts constituent topological modules. The platform offers interactive topology visualization graphs.ConclusionProLego, provides an alternative but comprehensive way to scan and visualize protein topology along with an extensive database of protein topology. ProLego can be found at http://www.proteinlego.comElectronic supplementary materialThe online version of this article (10.1186/s12859-018-2171-9) contains supplementary material, which is available to authorized users.

show abstract

“…The consistent observation of 80/20 rule in topology space is perceptible as shown by Figure 1 and Figure S5. This can be drawn in parallel to "Paretodistribution" that is eminent in across fields of natural sciences and economics [21,22]. The variance in protein space in "Prevalent" and "Non-prevalent" groups are majorly influence by the nature of "structure class".…”

Section: Distribution Of Proteins In Topology Spacementioning

confidence: 98%

ProLego: tool for extracting and visualizing topological modules in protein structures

Khan

Panday

Ghosh

2017

Preprint

View full text Add to dashboard Cite

BackgroundIn protein design, correct use of topology is among the initial and most critical feature. Meticulous selection of backbone topology aids in drastically reducing the structure search space. With ProLego, we present a server application to explore the component aspect of protein structures and provide an intuitive and efficient way to scan the protein topology space. ResultWe have implemented in-house developed "topological representation" in an automatedpipeline to extract protein topology from given protein structure. Using the topology string, ProLego, compares topology against a non-redundant extensive topology database (ProLegoDB) as well as extracts constituent topological modules. The platform offers interactive topology visualization graphs. ConclusionProLego, provides an alternative but comprehensive way to scan and visualize protein topology along with an extensive database of protein topology.ProLego can be found at http://www.proteinlego.com

show abstract

Searching for the Pareto frontier in multi-objective protein design

Cited by 6 publications

References 50 publications

How electrostatic networks modulate specificity and stability of collagen

How electrostatic networks modulate specificity and stability of collagen

ProLego: tool for extracting and visualizing topological modules in protein structures

ProLego: tool for extracting and visualizing topological modules in protein structures

Contact Info

Product

Resources

About