Computer-aided molecular design using Tabu search

Lin, Bao; Chavali, Sunitha; Camarda, Kyle V.; Miller, David C.

doi:10.1016/j.compchemeng.2004.10.008

Cited by 59 publications

(34 citation statements)

References 26 publications

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“…Error estimation for the properties predicted by the QSPRs was performed using prediction intervals (Wasserman, 2004). For solution of the inverse (product design) problem, the QSPRs were used in a CMD framework utilizing a stochastic optimization method known as Tabu search to select candidate molecules with property values estimated to match prespecified targets (Eslick et al, 2009; Glover, 1990; Lin, Chavali, Camarda, & Miller, 2005). Prediction intervals were used to compare locally optimal solutions generated from Tabu search, to the authors’ knowledge providing the first attempt at statistical comparison of locally optimal solutions in computational molecular design.…”

Section: Introductionmentioning

confidence: 99%

Use of glass transitions in carbohydrate excipient design for lyophilized protein formulations

Roughton¹,

Topp²,

Camarda³

2012

Computers & Chemical Engineering

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This work describes an effort to apply methods from process systems engineering to a pharmaceutical product design problem, with a novel application of statistical approaches to comparing solutions. A computational molecular design framework was employed to design carbohydrate molecules with high glass transition temperatures and low water content in the maximally freeze-concentrated matrix, with the objective of stabilizing lyophilized protein formulations. Quantitative structure–property relationships were developed for glass transition temperature of the anhydrous solute, glass transition temperature of the maximally concentrated solute, melting point of ice and Gordon–Taylor constant for carbohydrates. An optimization problem was formulated to design an excipient with optimal property values. Use of a stochastic optimization algorithm, Tabu search, provided several carbohydrate excipient candidates with statistically similar property values, as indicated by prediction intervals calculated for each property.

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Section: Introductionmentioning

confidence: 99%

Use of glass transitions in carbohydrate excipient design for lyophilized protein formulations

Roughton¹,

Topp²,

Camarda³

2012

Computers & Chemical Engineering

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“…Lin et al studied the design of metal catalysts [15], numerous articles can be found for the design of drugs [5,[16][17][18], Perdomo et al designed and improved biodiesel fuel blends [3] and Kasat et al summarized the applications of genetic algorithms in polymer science including polymer design [2].…”

Section: Problem Formulationmentioning

confidence: 99%

“…Genetic algorithms (GA) are used in several publications [15,19,20], a combination of neural networks and genetic algorithms is used in [21] and linear programming is used in [12,14]. …”

Section: Problem Formulationmentioning

confidence: 99%

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Group Contribution Method-based Multi-objective Evolutionary Molecular Design

Dörgő¹,

Abonyi²

2016

Hungarian Journal of Industry and Chemistry

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The search for compounds exhibiting desired physical and chemical properties is an essential, yet complex problem in the chemical, petrochemical, and pharmaceutical industries. During the formulation of this optimization-based design problem two tasks must be taken into consideration: the automated generation of feasible molecular structures and the estimation of macroscopic properties based on the resultant structures. For this structural characteristic-based property prediction task numerous methods are available. However, the inverse problem, the design of a chemical compound exhibiting a set of desired properties from a given set of fragments is not so well studied. Since in general design problems molecular structures exhibiting several and sometimes conflicting properties should be optimized, we proposed a methodology based on the modification of the multi-objective Non-dominated Sorting Genetic Algorithm-II (NSGA-II). The originally huge chemical search space is conveniently described by the Joback estimation method. The efficiency of the algorithm was enhanced by soft and hard structural constraints, which expedite the search for feasible molecules. These constraints are related to the number of available groups (fragments), the octet rule and the validity of the branches in the molecule. These constraints are also used to introduce a special genetic operator that improves the individuals of the populations to ensure the estimation of the properties is based on only reliable structures. The applicability of the proposed method is tested on several benchmark problems.

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“…Chavali et al demonstrated that 2D connectivity indexes are useful for generating structure-property correlations for biological and chemical properties in reactions catalysed by transition metals. [64,65] These tools were applied in the Computer Aided Molecular Design (CAMD) environment, a powerful computational tool used in product design. The method uses optimization techniques coupled with molecular design and property estimation methods, generating those molecular structures that match a desired set of properties.…”

Section: D and 1d Descriptorsmentioning

confidence: 99%

In Silico Design in Homogeneous Catalysis Using Descriptor Modelling

Burello

Rothenberg

2006

IJMS

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This review summarises the state-of-the-art methodologies used for designing homogeneous catalysts and optimising reaction conditions (e.g. choosing the right solvent). We focus on computational techniques that can complement the current advances in highthroughput experimentation, covering the literature in the period 1996-2006. The review assesses the use of molecular modelling tools, from descriptor models based on semiempirical and molecular mechanics calculations, to 2D topological descriptors and graph theory methods. Different techniques are compared based on their computational and time cost, output level, problem relevance and viability. We also review the application of various data mining tools, including artificial neural networks, linear regression, and classification trees. The future of homogeneous catalysis discovery and optimisation is discussed in the light of these developments.

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Computer-aided molecular design using Tabu search

Cited by 59 publications

References 26 publications

Use of glass transitions in carbohydrate excipient design for lyophilized protein formulations

Use of glass transitions in carbohydrate excipient design for lyophilized protein formulations

Group Contribution Method-based Multi-objective Evolutionary Molecular Design

In Silico Design in Homogeneous Catalysis Using Descriptor Modelling

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