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Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding.

Kalinowska B, Fabian P, Stąpor K, Roterman I - J. Comput. Aided Mol. Des. (2015)

Bottom Line: The scientific community has recently devoted much attention to early stages of this process, with numerous attempts at simulating them--either experimentally or in silico.This paper presents a comparative analysis of the predicted and observed results of folding simulations.The proposed technique, based on statistical dictionaries, yields a global accuracy of 57%--a marked improvement over older approaches (with an accuracy of approximately 46%).

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Lazarza 16, Krakow, Poland.

ABSTRACT
The polypeptide chain folding process appears to be a multi-stage phenomenon. The scientific community has recently devoted much attention to early stages of this process, with numerous attempts at simulating them--either experimentally or in silico. This paper presents a comparative analysis of the predicted and observed results of folding simulations. The proposed technique, based on statistical dictionaries, yields a global accuracy of 57%--a marked improvement over older approaches (with an accuracy of approximately 46%).

No MeSH data available.


Probability distribution profiles for (φe, ψe) values for histidine, along with structural codes corresponding to individual maxima. The t parameter traverses the elliptical path starting with one of its poles which is located in the bottom right-hand corner of the Ramachandran plot. Bars represent the specific placement of all seven probability maxima which are used to express the early stage intermediate structure
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Fig2: Probability distribution profiles for (φe, ψe) values for histidine, along with structural codes corresponding to individual maxima. The t parameter traverses the elliptical path starting with one of its poles which is located in the bottom right-hand corner of the Ramachandran plot. Bars represent the specific placement of all seven probability maxima which are used to express the early stage intermediate structure

Mentions: If each observed pair of (φ, ψ) angles is projected onto the limited subspace using the minimum distance criterion, the distribution of the resulting pairs (φe, ψe) can be shown to exhibit seven distinct maxima (Fig. 2). The areas corresponding to each local maximum can be translated into a structural code, resulting in a structural alphabet which consists of seven letters (A–G). This alphabet enables us to express the predicted structure of the ES intermediate with the precision of limited conformational sub-space.Fig. 2


Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding.

Kalinowska B, Fabian P, Stąpor K, Roterman I - J. Comput. Aided Mol. Des. (2015)

Probability distribution profiles for (φe, ψe) values for histidine, along with structural codes corresponding to individual maxima. The t parameter traverses the elliptical path starting with one of its poles which is located in the bottom right-hand corner of the Ramachandran plot. Bars represent the specific placement of all seven probability maxima which are used to express the early stage intermediate structure
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4491364&req=5

Fig2: Probability distribution profiles for (φe, ψe) values for histidine, along with structural codes corresponding to individual maxima. The t parameter traverses the elliptical path starting with one of its poles which is located in the bottom right-hand corner of the Ramachandran plot. Bars represent the specific placement of all seven probability maxima which are used to express the early stage intermediate structure
Mentions: If each observed pair of (φ, ψ) angles is projected onto the limited subspace using the minimum distance criterion, the distribution of the resulting pairs (φe, ψe) can be shown to exhibit seven distinct maxima (Fig. 2). The areas corresponding to each local maximum can be translated into a structural code, resulting in a structural alphabet which consists of seven letters (A–G). This alphabet enables us to express the predicted structure of the ES intermediate with the precision of limited conformational sub-space.Fig. 2

Bottom Line: The scientific community has recently devoted much attention to early stages of this process, with numerous attempts at simulating them--either experimentally or in silico.This paper presents a comparative analysis of the predicted and observed results of folding simulations.The proposed technique, based on statistical dictionaries, yields a global accuracy of 57%--a marked improvement over older approaches (with an accuracy of approximately 46%).

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Lazarza 16, Krakow, Poland.

ABSTRACT
The polypeptide chain folding process appears to be a multi-stage phenomenon. The scientific community has recently devoted much attention to early stages of this process, with numerous attempts at simulating them--either experimentally or in silico. This paper presents a comparative analysis of the predicted and observed results of folding simulations. The proposed technique, based on statistical dictionaries, yields a global accuracy of 57%--a marked improvement over older approaches (with an accuracy of approximately 46%).

No MeSH data available.