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.

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.

Automated Design of Image Operators that Detect Interest Points

2008 ◽  
Vol 16 (4) ◽  
pp. 483-507 ◽  
Author(s):  
Leonardo Trujillo ◽  
Gustavo Olague
Keyword(s):  
Computer Vision ◽  
Search Space ◽  
Search Problem ◽  
Interest Points ◽  
Fitness Evaluation ◽  
Modern Computer ◽  
New Perspective ◽  
Processing Techniques ◽  
Point Detection ◽  
Optimization Search

This work describes how evolutionary computation can be used to synthesize low-level image operators that detect interesting points on digital images. Interest point detection is an essential part of many modern computer vision systems that solve tasks such as object recognition, stereo correspondence, and image indexing, to name but a few. The design of the specialized operators is posed as an optimization/search problem that is solved with genetic programming (GP), a strategy still mostly unexplored by the computer vision community. The proposed approach automatically synthesizes operators that are competitive with state-of-the-art designs, taking into account an operator's geometric stability and the global separability of detected points during fitness evaluation. The GP search space is defined using simple primitive operations that are commonly found in point detectors proposed by the vision community. The experiments described in this paper extend previous results (Trujillo and Olague, 2006a,b) by presenting 15 new operators that were synthesized through the GP-based search. Some of the synthesized operators can be regarded as improved manmade designs because they employ well-known image processing techniques and achieve highly competitive performance. On the other hand, since the GP search also generates what can be considered as unconventional operators for point detection, these results provide a new perspective to feature extraction research.

scholarly journals Pengaruh Minimisasi Energi MMFF94 dengan MarvinSketch dan Open Babel PyRx pada Penambatan Molekular Turunan Oksindola Tersubstitusi

ALCHEMY ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 33-40
Author(s):  
Atika Umi Hanif ◽  
Prima Agusti Lukis ◽  
Arif Fadlan
Keyword(s):  
Molecular Docking ◽  
Drug Discovery ◽  
Force Field ◽  
Binding Affinity ◽  
Energy Minimization ◽  
In Silico ◽  
Initial State ◽  
Molecular Force ◽  
Molecular Force Field ◽  
Docking Energy

 In silico technique is widely used for drug discovery because it can predict the conformation of ligands in protein macromolecules and it can calculate the binding affinity. The energy minimization is carried out to make the ligand more stable near the initial state during molecular docking process. The Merck Molecular Force Field (MMFF94) is one type of energy minimization process often used in organic compounds. The molecular docking of substituted oxindole derivatives on indoleamine macromolecules 2,3-dioxygenase (IDO-1, PDB: 2D0T) by MMFF94 minimization operated by MarvinSketch and Open Babel in PyRx showed different results. The binding affinity energy obtained was also quite different, but the ligands have the same conformation and bind the same residue with slightly different bond distances. Keywords: Molecular docking, energy minimization, substituted oxindole, Merck Molecular Force Field 94  Teknik in silico banyak digunakan untuk penemuan senyawa obat karena dapat memprediksi konformasi suatu ligan dalam makromolekul protein dan mampu menghitung nilai afinitas ikatan. Proses minimisasi energi dilakukan untuk menjadikan ligan lebih stabil mendekati keadaan awal selama penambatan molekular berlangsung. Merck Molecular Force Field (MMFF94) adalah salah satu jenis persamaan minimisasi energi yang sering digunakan pada senyawa organik. Hasil pengujian pengaruh minimisasi energi dengan MMFF94 menggunakan program MarvinSketch dan Open Babel dalam PyRx pada turunan oksindola tersubstitusi alkil terhadap makromolekul 2,3-dioxygenase indoleamine (IDO-1, PDB: 2D0T) menunjukkan hasil dengan nilai yang berbeda. Energi afinitas ikatan yang didapatkan juga cukup berbeda, namun ligan memiliki konformasi yang sama dan mengikat residu yang sama dengan jarak ikatan yang sedikit berbeda. Kata kunci: Penambatan molekular, minimisasi energi, oksindola tersubstitusi, Merck Molecular Force Field 94

scholarly journals Variable Neighbourhood Search

2003 ◽  
Vol 7 (19) ◽  
Author(s):  
P. Hansen ◽  
N. Mladenovic ◽  
J.A. Moreno
Keyword(s):  
Variable Neighbourhood Search ◽  
Neighbourhood Search

Spatial Structure of the Acth-(6-9)-PGP Molecule

2021 ◽  
Vol 43 (5) ◽  
pp. 500-500
Author(s):  
Namiq Akhmedov Namiq Akhmedov ◽  
Leyla Agayeva Leyla Agayeva ◽  
Gulnara Akverdieva Gulnara Akverdieva ◽  
Rena Abbasli and Larisa Ismailova Rena Abbasli and Larisa Ismailova
Keyword(s):  
Amino Acid ◽  
Spatial Structure ◽  
Main Chain ◽  
Low Energy ◽  
Dihedral Angles ◽  
Amino Acid Residues ◽  
Analysis Method ◽  
Theoretical Conformational Analysis ◽  
Energy Of Hydrogen Bonds ◽  
Low Energy Conformations

The spatial structure of ACTH-(6-9)-PGP molecule has been investigated using theoretical conformational analysis method. Amino acid sequence of the N-terminal pentapeptide fragment of His-Phe-Arg-Trp-Pro of this molecule conforms to the fragment 6-9 of ACTH hormone. Calculations of conformational states of this molecule are carried out regarding nonvalent, electrostatic and torsional interactions and the energy of hydrogen bonds. The spatial structure of the His-Phe-Arg-Trp-Pro-Gly-Pro molecule was estimated on the low–energy conformations of the N-terminal tetrapeptide fragment His-Phe-Arg-Trp and C-terminal tripeptide fragment Pro-Gly-Pro of this molecule. It is shown that the spatial structure of heptapeptide molecule can be presented by 11 low-energy forms of the main chain. The low–energy conformations of this molecule, the values of dihedral angles of the backbone and side chains of the amino acid residues were founded and the energies of intra- and inter-residual interactions were determined.

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