Decolonizing Otherness through a Transcultural Lens: Conclusion

Research output: Contributions to collected editions/worksContributions to collected editions/anthologiesResearch

Standard

Decolonizing Otherness through a Transcultural Lens: Conclusion. / Gaupp, Lisa.

Diversity and Otherness: Transcultural Insights into Norms, Practices, Negotiations. ed. / Lisa Gaupp; Giulia Pelillo-Hestermeyer. Berlin : Walter de Gruyter GmbH, 2021. p. 336-355.

Research output: Contributions to collected editions/worksContributions to collected editions/anthologiesResearch

Harvard

Gaupp, L 2021, Decolonizing Otherness through a Transcultural Lens: Conclusion. in L Gaupp & G Pelillo-Hestermeyer (eds), Diversity and Otherness: Transcultural Insights into Norms, Practices, Negotiations. Walter de Gruyter GmbH, Berlin, pp. 336-355. https://doi.org/10.1515/9788366675308-016

APA

Gaupp, L. (2021). Decolonizing Otherness through a Transcultural Lens: Conclusion. In L. Gaupp, & G. Pelillo-Hestermeyer (Eds.), Diversity and Otherness: Transcultural Insights into Norms, Practices, Negotiations (pp. 336-355). Walter de Gruyter GmbH. https://doi.org/10.1515/9788366675308-016

Vancouver

Gaupp L. Decolonizing Otherness through a Transcultural Lens: Conclusion. In Gaupp L, Pelillo-Hestermeyer G, editors, Diversity and Otherness: Transcultural Insights into Norms, Practices, Negotiations. Berlin: Walter de Gruyter GmbH. 2021. p. 336-355 doi: 10.1515/9788366675308-016

Bibtex

@inbook{5f0c3a1ebdbe4b81bfc071f7d6000b9c,
title = "Decolonizing Otherness through a Transcultural Lens: Conclusion",
abstract = "Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-α-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 {\AA} for the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40% of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.",
keywords = "Gender and Diversity, Cultural studies",
author = "Lisa Gaupp",
year = "2021",
month = dec,
day = "31",
doi = "10.1515/9788366675308-016",
language = "English",
isbn = "978-83-66675-29-2",
pages = "336--355",
editor = "Lisa Gaupp and Giulia Pelillo-Hestermeyer",
booktitle = "Diversity and Otherness",
publisher = "Walter de Gruyter GmbH",
address = "Germany",

}

RIS

TY - CHAP

T1 - Decolonizing Otherness through a Transcultural Lens: Conclusion

AU - Gaupp, Lisa

PY - 2021/12/31

Y1 - 2021/12/31

N2 - Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-α-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 Å for the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40% of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.

AB - Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-α-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 Å for the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40% of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.

KW - Gender and Diversity

KW - Cultural studies

UR - https://www.mendeley.com/catalogue/70f0c997-d034-3f0b-a2cd-7cc8efa28b85/

U2 - 10.1515/9788366675308-016

DO - 10.1515/9788366675308-016

M3 - Contributions to collected editions/anthologies

SN - 978-83-66675-29-2

SP - 336

EP - 355

BT - Diversity and Otherness

A2 - Gaupp, Lisa

A2 - Pelillo-Hestermeyer, Giulia

PB - Walter de Gruyter GmbH

CY - Berlin

ER -