A path planning-based study of protein folding with a case study of hairpin formation in protein G and L

Guang Song; Shawna Thomas; Ken A Dill; J Martin Scholtz; Nancy M Amato

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Conference proceeding

A path planning-based study of protein folding with a case study of hairpin formation in protein G and L

Guang Song, Shawna Thomas, Ken A Dill, J Martin Scholtz and Nancy M Amato

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Vol.8, pp.240-251

2003

PMID: 12603032

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Abstract

We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMS). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structure, assuming we know the native fold. A feature of our PRM-based framework is that the large sets of folding pathways in the roadmaps it produces, in a few hours on a desktop PC, provide global information about the protein's energy landscape. This is an advantage over other simulation methods such as molecular dynamics or Monte Carlo methods which require more computation and produce only a single trajectory in each run. In our initial studies, we obtained encouraging results for several small proteins. In this paper, we investigate more sophisticated techniques for analyzing the folding pathways in our roadmaps. In addition to more formally revalidating our previous results, we present a case study showing our technique captures known folding differences between the structurally similar proteins G and L.

Protein Folding

Thermodynamics

Bacterial Proteins

Computer Simulation

DNA-Binding Proteins - chemistry

Models, Molecular

Models, Statistical

Monte Carlo Method

Nerve Tissue Proteins - chemistry

Protein Structure, Secondary

Details

Title: Subtitle: A path planning-based study of protein folding with a case study of hairpin formation in protein G and L
Creators: Guang Song - Department of Computer Science, Texas A&M University, College Station, TX 77843-3112, USA. gsong@cs.tamu.edu
Shawna Thomas
Ken A Dill
J Martin Scholtz
Nancy M Amato
Resource Type: Conference proceeding
Publication Details: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Vol.8, pp.240-251
PMID: 12603032
ISSN: 2335-6936
Language: English
Date published: 2003
Academic Unit: Research Administration; Pharmaceutical Sciences and Experimental Therapeutics; Biochemistry and Molecular Biology; Chemistry
Record Identifier: 9984293076302771

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