PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution

J Rey, S Murail, S de Vries, P Derreumaux… - Nucleic Acids …, 2023 - academic.oup.com
J Rey, S Murail, S de Vries, P Derreumaux, P Tuffery
Nucleic Acids Research, 2023academic.oup.com
Accurate and fast structure prediction of peptides of less 40 amino acids in aqueous solution
has many biological applications, but their conformations are pH-and salt concentration-
dependent. In this work, we present PEP-FOLD4 which goes one step beyond many
machine-learning approaches, such as AlphaFold2, TrRosetta and RaptorX. Adding the
Debye-Hueckel formalism for charged-charged side chain interactions to a Mie formalism for
all intramolecular (backbone and side chain) interactions, PEP-FOLD4, based on a coarse …
Abstract
Accurate and fast structure prediction of peptides of less 40 amino acids in aqueous solution has many biological applications, but their conformations are pH- and salt concentration-dependent. In this work, we present PEP-FOLD4 which goes one step beyond many machine-learning approaches, such as AlphaFold2, TrRosetta and RaptorX. Adding the Debye-Hueckel formalism for charged-charged side chain interactions to a Mie formalism for all intramolecular (backbone and side chain) interactions, PEP-FOLD4, based on a coarse-grained representation of the peptides, performs as well as machine-learning methods on well-structured peptides, but displays significant improvements for poly-charged peptides. PEP-FOLD4 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4. This server is free and there is no login requirement.
Oxford University Press
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