Refinement of reduced protein models with all-atom force fields - Ph.D. Defense

Wróblewska, Liliana

Title:

Refinement of reduced protein models with all-atom force fields - Ph.D. Defense

dc.contributor.advisor	Skolnick, Jeffrey
dc.contributor.author	Wróblewska, Liliana
dc.contributor.committeeMember	Facundo M. Fernandez
dc.contributor.committeeMember	Jordan, I. King
dc.contributor.committeeMember	John McDonald
dc.contributor.committeeMember	David C. Sherrill
dc.contributor.department	Biology
dc.date.accessioned	2007-12-11T19:31:58Z
dc.date.available	2007-12-11T19:31:58Z
dc.date.issued	2007-10-30
dc.description	This is the Ph.D. defense for the dissertation "Refinement of reduced protein models with all-atom force fields", located here: http://hdl.handle.net/1853/26606
dc.description	Runtime: 58:59 minutes
dc.description.abstract	The goal of the following thesis research was to develop a systematic approach for the refinement of low-resolution protein models, as a part of the protein structure prediction procedure. Significant progress has been made in the field of protein structure prediction and the contemporary methods are able to assemble correct topology for a large fraction of protein domains. But such approximate models are often not detailed enough for some important applications, including studies of reaction mechanisms, functional annotation, drug design or virtual ligand screening. The development of a method that could bring those structures closer to the native is then of great importance. The minimal requirements for a potential that can refine protein structures is the existence of a correlation between the energy with native similarity and the scoring of the native structure as being lowest in energy. Extensive tests of the contemporary all-atom physics-based force fields were conducted to assess their applicability for refinement. The tests revealed flatness of such potentials and enabled the identification of the key problems in the current approaches. Guided by these results, the optimization of the AMBER (ff03) force field was performed that aimed at creating a funnel shape of the potential, with the native structure at the global minimum. Such shape should facilitate the conformational search during refinement and drive it towards the native conformation. Adjusting the relative weights of particular energy components, and adding an explicit hydrogen bond potential significantly improved the average correlation coefficient of the energy with native similarity (from 0.25 for the original ff03 potential to 0.65 for the optimized force field). The fraction of proteins for which the native structure had lowest energy increased from 0.22 to 0.90. The new, optimized potential was subsequently used to refine protein models of various native-similarity. The test employed 47 proteins and 100 decoy structures per protein. When the lowest energy structure from each trajectory was compared with the starting decoy, we observed structural improvement for 70% of the models on average. Such an unprecedented result of a systematic refinement is extremely promising in the context of high-resolution structure prediction.	en_US
dc.description.degree	Ph.D.
dc.format.extent	58:59 minutes
dc.identifier.uri	http://hdl.handle.net/1853/18356
dc.language.iso	en_US	en_US
dc.publisher	Georgia Institute of Technology	en_US
dc.relation.isbasedon	http://hdl.handle.net/1853/26606
dc.subject	Force field optimization	en_US
dc.subject	Decoy scoring	en_US
dc.subject	Protein structure prediction	en_US
dc.subject	Protein model refinement	en_US
dc.title	Refinement of reduced protein models with all-atom force fields - Ph.D. Defense	en_US
dc.type	Moving Image
dc.type	Text
dc.type.genre	Presentation
dspace.entity.type	Publication
local.contributor.advisor	Skolnick, Jeffrey
local.contributor.corporatename	College of Sciences
local.contributor.corporatename	School of Biological Sciences
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