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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.


2VAD structure (A chain) a native structure derived from PDB, b structure obtained by projecting each (φ, ψ) angle pair onto the elliptical path which represents the ES conformational subspace, c ES structure obtained using the statistical dictionary method, d ES structure obtained using the contingency table method. Blue, red and green fragments correspond to residues which form α-helixes, β-twists and loops respectively. Source: PyMOL
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Fig6: 2VAD structure (A chain) a native structure derived from PDB, b structure obtained by projecting each (φ, ψ) angle pair onto the elliptical path which represents the ES conformational subspace, c ES structure obtained using the statistical dictionary method, d ES structure obtained using the contingency table method. Blue, red and green fragments correspond to residues which form α-helixes, β-twists and loops respectively. Source: PyMOL

Mentions: The final example is 2VAD for which the statistical dictionary method proved vastly superior to the contingency table method (85 vs. 35 %). This particular protein consists mainly of β-sheets; a structural motif for which the contingency table method produces poor results. Figure 6 highlights the differences between the outcome of each algorithm, with extended fragments corresponding to individual β-sheets. Another possible reason for the reduced accuracy of the contingency table method is the potential presence of a ligand, which distorts the protein’s conformation.Fig. 6


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)

2VAD structure (A chain) a native structure derived from PDB, b structure obtained by projecting each (φ, ψ) angle pair onto the elliptical path which represents the ES conformational subspace, c ES structure obtained using the statistical dictionary method, d ES structure obtained using the contingency table method. Blue, red and green fragments correspond to residues which form α-helixes, β-twists and loops respectively. Source: PyMOL
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig6: 2VAD structure (A chain) a native structure derived from PDB, b structure obtained by projecting each (φ, ψ) angle pair onto the elliptical path which represents the ES conformational subspace, c ES structure obtained using the statistical dictionary method, d ES structure obtained using the contingency table method. Blue, red and green fragments correspond to residues which form α-helixes, β-twists and loops respectively. Source: PyMOL
Mentions: The final example is 2VAD for which the statistical dictionary method proved vastly superior to the contingency table method (85 vs. 35 %). This particular protein consists mainly of β-sheets; a structural motif for which the contingency table method produces poor results. Figure 6 highlights the differences between the outcome of each algorithm, with extended fragments corresponding to individual β-sheets. Another possible reason for the reduced accuracy of the contingency table method is the potential presence of a ligand, which distorts the protein’s conformation.Fig. 6

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.