Comparison of residue motion correlation in BPTI using vacuum and solvent molecular dynamics simulations

مقدم أطروحة جامعية

al-Ajarmah, Basim

أعضاء اللجنة

Awad, Hani
Qarain, Wail
Hamid, Mazin Y.

الجامعة

جامعة بيرزيت

الكلية

كلية الهندسة و التكنولوجيا

القسم الأكاديمي

دائرة علم الحاسوب

دولة الجامعة

فلسطين (الضفة الغربية)

الدرجة العلمية

ماجستير

تاريخ الدرجة العلمية

2005

الملخص الإنجليزي

Correlated motions in protein molecules play a very important role in the function of the protein.

The method of essential dynamics was used in this work to study these correlated motions in the protein Bovine Pancreatic Trypsin Inhibitor (BPTI).

Molecular dynamics trajectories were simulated using the program NAMD both in solution and in vacuum for 20 ns.

Several diagnostic tests were performed on the trajectories: RMSD, temperature factor, correlation maps, and essential dynamics (PCA) analysis as well.

The results were compared for the two environments, and inspected for their behavior versus time.

The main contribution of this work is that this is the longest reported simulation for this protein and ores new insights into how the atoms of the protein behave versus time for "long" simulations.

التخصصات الرئيسية

تكنولوجيا المعلومات وعلم الحاسوب

الموضوعات

• الجزيئات

عدد الصفحات

168

قائمة المحتويات

• APA
• MLA
• AMA

لغة النص

الإنجليزية

نوع البيانات

رسائل جامعية

رقم السجل

BIM-303443