Convergence of conformational sampling for BPTI in a 30ns molecular dynamics simulation
Dissertant
al-Hausani, Wasim Ahmad Muhammad
Comitee Members
Hamad, Mazin Y.
Qarain, Wail
al-Kafri, Wasfi
University
Birzeit University
Faculty
Faculty of Engineering and Technology
Department
Department of Computer Science
University Country
Palestine (West Bank)
Degree
Master
Degree Date
2007
English Abstract
Studying protein intermolecular motion gives an important knowledge about its function.
In this work, the convergence of the conformational sampling space was performed on a 30ns long molecular dynamics simulation of Bovine Pancreatic Trypsin Inhibitor (BPTI).
The overlap between the principle component vectors for die rent time windows of the simulation time were calculated using two methods.
The rest method measures the total overlap between covariance matrices of die rent time segments.
It shows a lack of convergence with steady values throughout the simulation.
The second method examines the subspace overlap between eigenvectors of die rent time windows of simulation.
This method shows high convergence between 4ns long time fragments.
The most of atomic actuations of BPTIC atoms can be seen in 4ns time intervals.
The B-factor and RMSD were calculated in water to check the validity of the simulation results.
They give good agreement with the experiment.
Main Subjects
Topics
No. of Pages
96
Table of Contents
Abstract.
Table of contents.
Chapter one : Introduction.
Chapter two : Theoretical background and used techniques.
Chapter three : Computing tools and methodology.
Chapter four : Results and analysis.
Chapter five : Discussion of results and conclusion.
References.
American Psychological Association (APA)
al-Hausani, Wasim Ahmad Muhammad. (2007). Convergence of conformational sampling for BPTI in a 30ns molecular dynamics simulation. (Master's theses Theses and Dissertations Master). Birzeit University, Palestine (West Bank)
https://search.emarefa.net/detail/BIM-303397
Modern Language Association (MLA)
al-Hausani, Wasim Ahmad Muhammad. Convergence of conformational sampling for BPTI in a 30ns molecular dynamics simulation. (Master's theses Theses and Dissertations Master). Birzeit University. (2007).
https://search.emarefa.net/detail/BIM-303397
American Medical Association (AMA)
al-Hausani, Wasim Ahmad Muhammad. (2007). Convergence of conformational sampling for BPTI in a 30ns molecular dynamics simulation. (Master's theses Theses and Dissertations Master). Birzeit University, Palestine (West Bank)
https://search.emarefa.net/detail/BIM-303397
Language
English
Data Type
Arab Theses
Record ID
BIM-303397
