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Predicting three-dimensional structure of protein fragments from dihedral angle propensities and molecular dynamics

Blayney, Jaine K ; Ojha, Piyush C ; Shapcott, Mary

International journal of computational biology and drug design, 2010, Vol.3 (2), p.146-163 [Periódico revisado por pares]

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Título:
Predicting three-dimensional structure of protein fragments from dihedral angle propensities and molecular dynamics
Autor: Blayney, Jaine K ; Ojha, Piyush C ; Shapcott, Mary
Assuntos: Algorithms ; Amino Acid Sequence ; Amino Acids - chemistry ; Computational Biology - methods ; Peptides - chemistry ; Protein Stability ; Protein Structure, Tertiary ; Proteins - chemistry
É parte de: International journal of computational biology and drug design, 2010, Vol.3 (2), p.146-163
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Descrição: Incorporating the existing knowledge of protein structural preferences, e.g., amino acid angle frequencies, in structure prediction have proven to be less successful with smaller peptides. In this work, we compare the effectiveness of backbone angle propensity libraries derived from two protein data sets: one consisting of proteins of unrestricted lengths; the second containing proteins ranging in size from 40 to 75 residues. Model structures for 29 target peptides are predicted using a threading algorithm and their stability evaluated using in vacuo molecular dynamics simulations. Structures derived from the data set consisting of smaller proteins outperformed those developed from that unrestricted by protein length.
Editor: England
Idioma: Inglês

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