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.

A COMBINATION OF REPLICA EXCHANGE MONTE CARLO AND ENERGY LANDSCAPE PAVING ALGORITHMS TO INCREASE THE EFFECTIVENESS OF CONFORMATIONAL SAMPLING

2004 ◽  
Vol 15 (07) ◽  
pp. 933-937 ◽  
Author(s):  
HANDAN ARKIN
Keyword(s):  
Monte Carlo ◽  
Hybrid Algorithm ◽  
Energy Landscape ◽  
Monte Carlo Sampling ◽  
Replica Exchange ◽  
Conformational Sampling ◽  
Sampling Techniques ◽  
Replica Exchange Monte Carlo ◽  
Energy Landscape Paving ◽  
Low Energy Conformations

A combination of replica exchange Monte Carlo sampling techniques and energy landscape paving approach is presented. This hybrid algorithm combines the features of the energy landscape paving (ELP) and replica exchange methods (REM). I have tested its performance in studying the low-energy conformations of the benchmark peptide Met-enkephalin.

STUDIES OF FINDING LOW ENERGY CONFIGURATIONS IN OFF-LATTICE PROTEIN MODELS

2006 ◽  
Vol 05 (03) ◽  
pp. 587-594 ◽  
Author(s):  
JINGFA LIU ◽  
WENQI HUANG
Keyword(s):  
Lower Energy ◽  
Gradient Descent ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Ground States ◽  
Low Energy ◽  
Protein Models ◽  
Energy Configurations ◽  
Energy Landscape Paving ◽  
Lattice Protein Models

We studied two three-dimensional off-lattice protein models with two species of monomers, hydrophobic and hydrophilic. Low energy configurations in both models were optimized using the energy landscape paving (ELP) method and subsequent gradient descent. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. For all sequences with lengths 13 ≤ n ≤ 55, the algorithm finds states with lower energy than previously proposed putative ground states.

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.

scholarly journals A Variable Neighbourhood Descent Heuristic for Conformational Search Using a Quantum Annealer

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
D. J. J. Marchand ◽  
M. Noori ◽  
A. Roberts ◽  
G. Rosenberg ◽  
B. Woods ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Search Space ◽  
Low Energy ◽  
Conformational Search ◽  
Variable Neighbourhood Search ◽  
Search Problem ◽  
And Topology ◽  
Molecular Force ◽  
Neighbourhood Search ◽  
Low Energy Conformations

Abstract Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in in silico materials design and drug discovery. In this paper, we propose a variable neighbourhood search heuristic for the conformational search problem. Using the structure of a molecule, neighbourhoods are chosen to allow for the efficient use of a binary quadratic optimizer for conformational search. The method is flexible with respect to the choice of molecular force field and the number of discretization levels in the search space, and can be further generalized to take advantage of higher-order binary polynomial optimizers. It is well-suited for the use of devices such as quantum annealers. After carefully defining neighbourhoods, the method easily adapts to the size and topology of these devices, allowing for seamless scaling alongside their future improvements.

SIMULATIONS OF PEPTIDE MODELS IN A SOLVENT

2004 ◽  
Vol 15 (02) ◽  
pp. 223-231 ◽  
Author(s):  
HANDAN ARKIN
Keyword(s):  
Aqueous Solution ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Solvation Energy ◽  
Low Energy ◽  
Energy Term ◽  
Nmr Data ◽  
Peptide Models ◽  
Ramachandran Plots ◽  
Energy Landscape Paving

The three-dimensional structures of the heptapeptide deltorphin ( H - Tyr 1- D - Met 2- Phe 3- His 4- Leu 5- Met 6- Asp 7- NH 2) are studied in aqueous solution using Energy Landscape Paving (ELP) method. The effect of a solvation energy term on the conformations are determined by analyzing Ramachandran plots. The structures are compared with experimental NMR data. By minimizing the energy structures, the low-energy microstates of the molecule in aqueous solution are determined.

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