Decolonizing Otherness through a Transcultural Lens: Conclusion
Research output: Contributions to collected editions/works › Contributions to collected editions/anthologies › Research
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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/works › Contributions to collected editions/anthologies › Research
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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 -