Characterization of Antimicrobial and Host-Defense Peptides by NMR Spectroscopy

Vogel, Hans J.; Arias, Mauricio; Aramini, James M.; Paul, Subrata; Liu, Zhihong; Ishida, Hiroaki

doi:10.1007/978-3-319-28275-6_119-1

Cited by 1 publication

(1 citation statement)

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“…While ESA, as an ab initio calculation, is not restricted by this situation, which will support for the study of proteins lacking sequence homologues, such as antibody proteins and orphan proteins. For the study of peptide, conformational missing of computational results will cause difficulties in converting experiments into three-dimensional structures 80,81 and it will miss the active conformations, because of numerous states of existence of peptides caused by the high flexibility and the wide energy range distribution for the active conformations 34,35 . And the missing of the lowest free energy, will also cause invalid assessment on biological or chemical activities of the peptides 82 , which form complexes on important sites in proteins 45,46,83 , 84 .…”

Section: Discussionmentioning

confidence: 99%

A New Ab Initio Algorithm for Structure Prediction of Peptides, Theory, Software and Database

Xiao

Yao

et al. 2023

Preprint

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We present a new fragment-based algorithm to solve the problem of structural prediction for peptide molecules using ab initio calculation. We developed an operation of multilevel ensemble assembly derived from the theory of statistical physics and adopted the structural optimization at the quantum chemistry level. A novel scheme of ensemble acquisition with higher accuracy and completeness is developed specifically for the basic units that act as the initial elements. The ensemble property of fragments at the junction is used to judge the potential of individuals of each block ensemble for construction. The test results show our algorithm is better than the scheme of structure extraction from the Protein Data Bank, which is widely used in biology. We also establish a mathematical form to describe our algorithm and generalize to a framework of a theory appropriate for structural prediction for general linear molecules. Meanwhile, the trial version of this prediction software and peptide database is published.

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