eprintid: 30143
rev_number: 12
userid: 5901
dir: disk0/00/03/01/43
datestamp: 2016-11-22 17:45:08
lastmod: 2017-08-25 04:56:30
status_changed: 2016-11-22 17:45:08
type: conference_item
metadata_visibility: show
eprint_status: archive
creators_name: Yuan, Chenhui
creators_name: Koes, David
creators_email: 
creators_email: dkoes@pitt.edu
creators_id: 
creators_id: DKOES
creators_orcid: 
creators_orcid: 0000-0002-6892-6614
title: Computing free energies with PyBrella
ispublished: pub
divisions: sch_med_Computational_Systems_Biology
full_text_status: public
pres_type: poster
note: Funding: National Institutes of Health (NIH), GM108340-01 Competing Interests: No competing interests were disclosed
abstract: Calculations of the rates of disassociation between small molecules and proteins have numerous applications, including assisting rapid discovery and testing of novel drugs. Free energy calculations consider the enthalpy and entropy of the full protein-ligand-water system and so have the potential to be more accurate than faster, single-point calculations. In this study, methods are explored to predict the binding affinity of various molecules to proteins by molecular dynamics and umbrella sampling. An attempt was made to determine the potential of mean force (PMF) for the molecule, which was compared to its known binding capability. Factors including simulation resources, amounts of sampling, force strength parameters, and correlation between predicted energy and actual rate constants were considered in order to evaluate the umbrella sampling methods. Limitations in the simulation environment, such as the scaling of the PMF for sampling, biases in the SMD trajectory, and variations between ligands, were also investigated in the hope of creating a more comprehensive approach for predicting the target-molecule interaction.
date: 2014-05-20
date_type: published
publication: F1000 Research
publisher: F1000 Research Ltd.
event_title: 19th Annual International Conference on Research in Computational Molecular Biology (RECOMB) 2015
event_location: Warsaw, Poland
event_dates: 11 April 2015 - 15 April 2015
event_type: conference
refereed: FALSE
issn: 2046-1402
official_url: https://f1000research.com/posters/1095479
citation:   Yuan, Chenhui and Koes, David  (2014) Computing free energies with PyBrella.  In: 19th Annual International Conference on Research in Computational Molecular Biology (RECOMB) 2015, 11 April 2015 - 15 April 2015, Warsaw, Poland.     
document_url: http://d-scholarship-dev.library.pitt.edu/30143/1/f1000research-81474.pdf
document_url: http://d-scholarship-dev.library.pitt.edu/30143/7/licence.txt