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From Ramachandran Maps to Tertiary Structures of Proteins
The Journal of Physical Chemistry B, 2015Sequence to structure of proteins is an unsolved problem. A possible coarse grained resolution to this entails specification of all the torsional (Φ, Ψ) angles along the backbone of the polypeptide chain. The Ramachandran map quite elegantly depicts the allowed conformational (Φ, Ψ) space of proteins which is still very large for the purposes of ...
Debarati, DasGupta +2 more
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Principal component analysis in protein tertiary structure prediction
Journal of Bioinformatics and Computational Biology, 2018We discuss applicability of principal component analysis (PCA) for protein tertiary structure prediction from amino acid sequence. The algorithm presented in this paper belongs to the category of protein refinement models and involves establishing a low-dimensional space where the sampling (and optimization) is carried out via particle swarm optimizer (
Óscar, Álvarez +5 more
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Effect of methyl substitution on protein tertiary structure
Journal of Theoretical Biology, 1992Biological effects caused by the post-translational methylation of certain side chains in proteins has been thought to be due solely to changes in charge, steric relations or hydrophobicity at the site of the methyl group. However, there is increasing evidence that the presence of CH3 can also induce a "global" effect on the protein molecule.
W K, Paik, S, Kim
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CARBOHYDRATE-BINDING PROTEINS: TERTIARY STRUCTURES AND PROTEIN-SUGAR INTERACTIONS
Annual Review of Biochemistry, 1986PERSPECTIVES AND SUMMARY . 287 TERTIARY STRUCTURES 288 PROTEIN-SUGAR INTERACTIONS 292 Locations of Sugar-Binding Sites in Proteins 294 Hydrogen Bonds and van der Waals Contacts , 300 Oligosaccharide Binding ...
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Underlying Hydrophobic Sequence Periodicity of Protein Tertiary Structure
Journal of Biomolecular Structure and Dynamics, 2005Hydropathy plots or window averages over local stretches of the sequence of residue hydrophobicity have revealed patterns related to various protein tertiary structural features. This has enabled identification of regions of the sequence that are at the surface or within the interior of globular soluble proteins, regions located within the lipid ...
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Fast and accurate protein structure search with Foldseek
Nature Biotechnology, 2023Michel van Kempen +2 more
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Mechanisms, regulation and functions of the unfolded protein response
Nature Reviews Molecular Cell Biology, 2020Claudio Hetz +2 more
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