Folding simulations with novel conformational search method

2007 ◽  
Vol 126 (10) ◽  
pp. 104906 ◽  
Author(s):  
Won-Joon Son ◽  
Soonmin Jang ◽  
Youngshang Pak ◽  
Seokmin Shin
Keyword(s):  
Search Method ◽  
Conformational Search ◽  
Folding Simulations

scholarly journals A Conformational Search Method for Protein Systems Using Genetic Crossover and Metropolis Criterion

2014 ◽  
Vol 487 ◽  
pp. 012003 ◽  
Author(s):  
Yoshitake Sakae ◽  
Tomoyuki Hiroyasu ◽  
Mitsunori Miki ◽  
Katsuya Ishii ◽  
Yuko Okamoto
Keyword(s):  
Search Method ◽  
Conformational Search ◽  
Metropolis Criterion

scholarly journals Study on conformational search of new thiosemicarbazone reagent and complexes with metal ions integrating semi-empirical quantum and molecular mechanics calculation and Monte Carlo simulation

2020 ◽  
Vol 129 (1D) ◽  
Author(s):  
Nguyen Minh Quang ◽  
Tran Xuan Mau ◽  
Pham Van Tat ◽  
Pham Nu Ngoc Han
Keyword(s):  
Monte Carlo ◽  
Molecular Mechanics ◽  
Molecular System ◽  
Search Method ◽  
Conformational Search ◽  
Monte Carlo Techniques ◽  
Molecular Mechanics Calculation ◽  
Semi Empirical ◽  
Complexes With Metal Ions ◽  
Initial Selection

In this study, the conformational analysis of the ML2 complexes of new thiosemicarbazone reagents with metal cations Cd2+, Ni2+, Cu2+, Hg2+, Pb2+, Mn2+ and Zn2+ is to find the conformations with the most suitable energy of the whole molecular system. The search method incorporates MM+ and PM3 calculations with Monte Carlo techniques using the Metropolis algorithm in terms of T = 298K to 473K. The initial selection conformation was done randomly after 15 repeatable conformations and 30 conformations rejected. The conformations are chosen to change by changing the torsional-dihedral angle at the position of the metal cation associated with the donor atoms N and S of thiosemicarbazone reagents. The search method is performed by random changes of the dihedral angles to create new structures and then minimize the energy for each of these angles using molecular mechanics. The unique low energy suitability is stored while high or duplicate energy structures are discarded.

A FAST AND EFFECTIVE CONFORMATIONAL SEARCH METHOD FOR PEPTIDES

2003 ◽  
Vol 14 (07) ◽  
pp. 985-991 ◽  
Author(s):  
HANDAN ARKIN ◽  
TARIK ÇELIK
Keyword(s):  
Monte Carlo ◽  
Hybrid Algorithm ◽  
Energy Landscape ◽  
Search Method ◽  
Low Energy ◽  
Conformational Search ◽  
Energy Landscape Paving ◽  
Low Energy Conformations

We propose a hybrid algorithm, which combines the features of the energy landscape paving (ELP) and Monte Carlo Minimization (MCM) methods. We have tested its performance in studying the low-energy conformations of the heptapeptide deltorphin.

ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers

2010 ◽  
Vol 50 (4) ◽  
pp. 534-546 ◽  
Author(s):  
K. Shawn Watts ◽  
Pranav Dalal ◽  
Robert B. Murphy ◽  
Woody Sherman ◽  
Rich A. Friesner ◽  
...  
Keyword(s):  
Search Method ◽  
Conformational Search ◽  
Efficient Generation

Comparing the Conformational Behavior of a Series of Diastereomeric Cyclic Urea HIV-1 Inhibitors Using the Low Mode:Monte Carlo Conformational Search Method

2004 ◽  
Vol 47 (20) ◽  
pp. 4838-4850 ◽  
Author(s):  
Carol A. Parish ◽  
Matthew Yarger ◽  
Kent Sinclair ◽  
Myrianne Dure ◽  
Alla Goldberg
Keyword(s):  
Search Method ◽  
Conformational Search ◽  
Conformational Behavior ◽  
Hiv 1
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