J Comput Biol
Department of Chemistry, Duke University, Durham, North Carolina, USA.
Published: October 2024
D-peptides, the mirror image of canonical L-peptides, offer numerous biological advantages that make them effective therapeutics. This article details how to use DexDesign, the newest OSPREY-based algorithm, for designing these D-peptides . OSPREY physics-based models precisely mimic energy-equivariant reflection operations, enabling the generation of D-peptide scaffolds from L-peptide templates. Due to the scarcity of D-peptide:L-protein structural data, DexDesign calls a geometric hashing algorithm, Method of Accelerated Search for Tertiary Ensemble Representatives, as a subroutine to produce a synthetic structural dataset. DexDesign enables mixed-chirality designs with a new user interface and also reduces the conformation and sequence search space using three new design techniques: Minimum Flexible Set, Inverse Alanine Scanning, and K*-based Mutational Scanning.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11698684 | PMC |
http://dx.doi.org/10.1089/cmb.2024.0669 | DOI Listing |
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