Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures

Aleksandra E. Badaczewska-Dawid; Alisa Khramushin; Andrzej Kolinski; Ora Schueler-Furman; Sebastian Kmiecik

doi:10.1007/978-1-0716-0708-4_16

Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures

Aleksandra E. Badaczewska-Dawid
, Alisa Khramushin
, Andrzej Kolinski
, Ora Schueler-Furman
, Sebastian Kmiecik^*

^*Corresponding author for this work

Department of Microbiology and Molecular Genetics

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

5 Scopus citations

Abstract

Structural characterizations of protein–peptide complexes may require further improvements. These may include reconstruction of missing atoms and/or structure optimization leading to higher accuracy models. In this work, we describe a workflow that generates accurate structural models of peptide–protein complexes starting from protein–peptide models in C-alpha representation generated using CABS-dock molecular docking. First, protein–peptide models are reconstructed from their C-alpha traces to all-atom representation using MODELLER. Next, they are refined using Rosetta FlexPepDock. The described workflow allows for reliable all-atom reconstruction of CABS-dock models and their further improvement to high-resolution models.

Original language	English
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	273-287
Number of pages	15
DOIs	https://doi.org/10.1007/978-1-0716-0708-4_16
State	Published - 2020

Publication series

Name	Methods in Molecular Biology
Volume	2165
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Bibliographical note

Publisher Copyright:
© 2020, Springer Science+Business Media, LLC, part of Springer Nature.

Keywords

Coarse-grained model
Protein reconstruction
Protein refinement
Protein structure
Protein–peptide interaction

Access to Document

10.1007/978-1-0716-0708-4_16

Cite this

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abstract = "Structural characterizations of protein–peptide complexes may require further improvements. These may include reconstruction of missing atoms and/or structure optimization leading to higher accuracy models. In this work, we describe a workflow that generates accurate structural models of peptide–protein complexes starting from protein–peptide models in C-alpha representation generated using CABS-dock molecular docking. First, protein–peptide models are reconstructed from their C-alpha traces to all-atom representation using MODELLER. Next, they are refined using Rosetta FlexPepDock. The described workflow allows for reliable all-atom reconstruction of CABS-dock models and their further improvement to high-resolution models.",

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author = "Badaczewska-Dawid, \{Aleksandra E.\} and Alisa Khramushin and Andrzej Kolinski and Ora Schueler-Furman and Sebastian Kmiecik",

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Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures. / Badaczewska-Dawid, Aleksandra E.; Khramushin, Alisa; Kolinski, Andrzej et al.
Methods in Molecular Biology. Humana Press Inc., 2020. p. 273-287 (Methods in Molecular Biology; Vol. 2165).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

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AU - Schueler-Furman, Ora

AU - Kmiecik, Sebastian

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KW - Coarse-grained model

KW - Protein reconstruction

KW - Protein refinement

KW - Protein structure

KW - Protein–peptide interaction

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Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures

Abstract

Publication series

Bibliographical note

Keywords

Access to Document

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Cite this