Full Citation
Title: The rising marriage mortality gap among Whites
Citation Type: Miscellaneous
Publication Year: 2019
ISBN:
ISSN:
DOI: 10.31235/osf.io/8374m
NSFID:
PMCID:
PMID: 25246403
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 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.
Url: https://osf.io/preprints/socarxiv/8374m/
User Submitted?: No
Authors: Oliver, J.
Publisher: University of Maryland, College Park
Data Collections: IPUMS USA
Topics: Family and Marriage
Countries: United States