IDeAS: automated design tool for hetero-chiral protein folds

Incorporating D amino acids in the protein design alphabet can in principle multiply the design space by many orders of magnitude. All native proteins are polymers composed of L chiral amino acids. Practically limitless in diversity over amino acid sequences, protein structure is limited in folds an...

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Bibliographic Details
Published in:Physical biology 2018-08, Vol.15 (6), p.066005-066005
Main Authors: Ranbhor, Ranjit, Kumar, Anil, Tendulkar, Abhijit, Patel, Kirti, Ramakrishnan, Vibin, Durani, Susheel
Format: Article
Language:English
Subjects:
Amino Acids - chemistry
computational design
inverse design
Models, Molecular
Protein Folding
proteins
rotamer search
Software
stereochemistry
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Summary:Incorporating D amino acids in the protein design alphabet can in principle multiply the design space by many orders of magnitude. All native proteins are polymers composed of L chiral amino acids. Practically limitless in diversity over amino acid sequences, protein structure is limited in folds and thus shapes, principally due to the poly L stereochemistry of their backbone. To diversify shapes, we introduced both L- and D α-amino acids as design alphabets to explore the possibility of generating novel folds, varied in chemical as well as stereo-chemical sequence. Now, to have stereochemically-defined proteins tuned chemically, we present the Inverse Design and Automation Software, IDeAS. Retro-fitting side chains on a backbone with L and D stereochemistry, the software demonstrate functional fits over stereo-chemically diverse folds in a range of applications of interest in protein design.
ISSN:1478-3975
1478-3975
DOI:10.1088/1478-3975/aacdc3