New Tabu Search based global optimization methods outline of algorithms and study of efficiency

Stepanenko, S. V.; Engels, Bernd

doi:10.1002/jcc.20830

Cited by 21 publications

(33 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There exist other metaheuristic optimization algorithms which can also be employed for example the scatter search algorithm [30] or the tabu-searchbased algorithms. [31] We chose the simulated annealing approach due to its ability to quickly escape from local minima, which is very important considering the properties of the negative squared difference surface.…”

Section: Surface In the Refinement Processmentioning

confidence: 99%

Generation of Potential Energy Surfaces in High Dimensions and Their Haptic Exploration

2011

View full text Add to dashboard Cite

A method is proposed for the automated generation of potential energy surfaces in high dimensions. It combines the existing algorithm for the definition of new energy data points, based on the interpolating moving least-squares algorithm with a simulated annealing procedure. This method is then studied in a haptic quantum chemistry environment that requires a fast evaluation of gradients on a potential energy surface with automatic improvement of its accuracy. As an example we investigate the nitrogen binding pathway in the Schrock dinitrogen fixation complex with this set-up.

show abstract

Section: Surface In the Refinement Processmentioning

confidence: 99%

Generation of Potential Energy Surfaces in High Dimensions and Their Haptic Exploration

2011

View full text Add to dashboard Cite

show abstract

“…TS can handle non-differentiable objective functions, but the energy functions used in conformational sampling are typically continuous and differentiable, which allows to tailor the TS to such functions, for instance with the gradient tabu search [233] and variants [234]. So far, relatively few applications of TS to molecular conformational sampling questions have been presented, but TS has been tested for flexible ligand docking [235] and optimization of the conformational energy of the pentapeptide Met-enkephalin [236] (which has become a methodological test case [85,192,[237][238][239]).…”

Section: J Tabu Searchmentioning

confidence: 99%

Conformational Sampling and Energetics of Drug-Like Molecules

Foloppe

Chen²

2009

CMC

View full text Add to dashboard Cite

The pharmacological properties of small organic molecules depend on their three-dimensional (3D) structure. That includes physico-chemical properties (e.g. solubility, partition equilibria) and molecular recognition such as binding to a therapeutic macromolecular target. At physiological temperature, the 3D structure of a flexible small molecules is expected to cover an ensemble of energetically accessible conformations. Therefore, it is of fundamental and practical importance to be able to relate the energetics of a molecule to its conformational preferences and derived properties, a discipline known as conformational analysis. The first step of conformational analysis is the generation of the conformers, referred to as conformational sampling. This is typically performed primarily using computational chemistry methods. Taking a fresh look at these methods for a broad medicinal chemistry audience is the object of the present review. Indeed, conformational sampling methods continue to be developed, improved and tested. They underpin much of the detailed analysis of structure-activity relationships on selected chemical series, but also the preparation of large conformational libraries of generic compounds and their exploitation for virtual screening. In recent years, the conformational models of active compounds have been examined to see how frequently they capture their target-bound bioactive conformation, as revealed by X-ray crystallography. This provided a context to scrutinize the intrinsic conformational energetics of these bioactive conformers, but this subject is still intensely debated. Another line of investigation concerns the conformational diversity of the 3D models, and how well they cover the conformational and pharmacophoric spaces. This review addresses in general terms: i) the basic principles of conformational analysis, including modern computational estimates of intramolecular energy and how those are mapped on the molecular potential energy surface, ii) some experimental contributions to probing of the small molecule conformations, iii) the various computational methods available to generate conformational models, iv) the conformational properties of the bioactive conformers, and v) attempts to quantify the coverage of the conformational models and the controlling parameters.

show abstract

“…[63][64][65][66][67] To adopt the TS to the continuous conformational search problem, we developed several TS-based approaches. 68,69 Within these approaches, the gradient only TS (GOTS) turned out to be most efficient. 69,70 For the minimization step that launches a descent to the next local minimum, GOTS uses a Quasi-Newton method, combined with a steepest descent approach.…”

Section: Introductionmentioning

confidence: 99%

“…68,69 Within these approaches, the gradient only TS (GOTS) turned out to be most efficient. 69,70 For the minimization step that launches a descent to the next local minimum, GOTS uses a Quasi-Newton method, combined with a steepest descent approach. [71][72][73][74] To escape local minima, the GOTS uses grids of function values.…”

Section: Introductionmentioning

confidence: 99%

Efficiency of tabu‐search‐based conformational search algorithms

et al. 2011

Self Cite

View full text Add to dashboard Cite

Efficient conformational search or sampling approaches play an integral role in molecular modeling, leading to a strong demand for even faster and more reliable conformer search algorithms. This article compares the efficiency of a molecular dynamics method, a simulated annealing method, and the basin hopping (BH) approach (which are widely used in this field) with a previously suggested tabu-search-based approach called gradient only tabu search (GOTS). The study emphasizes the success of the GOTS procedure and, more importantly, shows that an approach which combines BH and GOTS outperforms the single methods in efficiency and speed. We also show that ring structures built by a hydrogen bond are useful as starting points for conformational search investigations of peptides and organic ligands with biological activities, especially in structures that contain multiple rings.

show abstract

New Tabu Search based global optimization methods outline of algorithms and study of efficiency

Cited by 21 publications

References 62 publications

Generation of Potential Energy Surfaces in High Dimensions and Their Haptic Exploration

Generation of Potential Energy Surfaces in High Dimensions and Their Haptic Exploration

Conformational Sampling and Energetics of Drug-Like Molecules

Efficiency of tabu‐search‐based conformational search algorithms

Contact Info

Product

Resources

About