Applications of soft computing in drug design

This review examines the role of soft computing methods such as artificial neural networks (ANNs), genetic algorithms (GAs), fuzzy logic (FL), chaos, fractals and cellular automata (CA) and their hybrids in the field of drug design. They have been found to be useful in a wide variety of areas including quantitative structure-activity relationship (QSAR), quantitative structure-property relationship (QSPR), variable selection, conformation searching, receptor docking, pharmacophore development, molecular design, combinatorial libraries, surface phenomena, kinetics and complex system studies. Based upon the studies examined, the use of soft computing techniques is likely to grow significantly in the future.

[1]  David E. Clark,et al.  Evolutionary algorithms in computer-aided molecular design , 1996, J. Comput. Aided Mol. Des..

[2]  Thomas E. Exner,et al.  New Docking Algorithm Based on Fuzzy Set Theory , 1997 .

[3]  S Hatrík,et al.  Neural Network Approach to the Prediction of the Toxicity of Benzothiazolium Salts from Molecular Structure , 1996, J. Chem. Inf. Comput. Sci..

[4]  Kimito Funatsu,et al.  GA Strategy for Variable Selection in QSAR Studies: GA-Based PLS Analysis of Calcium Channel Antagonists , 1997, J. Chem. Inf. Comput. Sci..

[5]  James Devillers,et al.  ART 2-A for Optimal Test Series Design in QSAR , 1997, J. Chem. Inf. Comput. Sci..

[6]  D. Maddalena,et al.  Applications of genetic algorithms to drug design , 1997 .

[7]  A. N. Jain,et al.  Quantitative binding site model generation: compass applied to multiple chemotypes targeting the 5-HT1A receptor. , 1995, Journal of medicinal chemistry.

[8]  Igor I. Baskin,et al.  A Neural Device for Searching Direct Correlations between Structures and Properties of Chemical Compounds , 1997, J. Chem. Inf. Comput. Sci..

[9]  Dezhao Chen,et al.  A Pattern Classification Procedure Integrating the Multivariate Statistical Analysis with Neural Networks , 1997, Comput. Chem..

[10]  M. Hosseini,et al.  Using Artificial Neural Networks To Classify the Activity of Capsaicin and Its Analogues , 1997, J. Chem. Inf. Comput. Sci..

[11]  Venkat Venkatasubramanian,et al.  Evolutionary Design of Molecules with Desired Properties Using the Genetic Algorithm , 1995, J. Chem. Inf. Comput. Sci..

[12]  César Hervás-Martínez,et al.  Computational Neural Networks in Conjunction with Principal Component Analysis for Resolving Highly Nonlinear Kinetics , 1997, J. Chem. Inf. Comput. Sci..

[13]  Jari Kyngäs,et al.  EVOLUTIONARY NEURAL NETWORKS IN QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS OF DIHYDROFOLATE REDUCTASE INHIBITORS , 1996 .

[14]  G. Kateman,et al.  Using Molecular Representations in Combination with Neural Networks. a Case Study: Prediction of the HPLC Retention Index , 1994, Comput. Chem..

[15]  Jean-Michel Cense,et al.  Prediction of the Impact Sensitivity by Neural Networks , 1996, J. Chem. Inf. Comput. Sci..

[16]  Guang Zhu,et al.  Using Neural Network Predicted Secondary Structure Information in Automatic Protein NMR Assignment , 1997, J. Chem. Inf. Comput. Sci..

[17]  Lotfi A. Zadeh,et al.  The Roles of Fuzzy Logic and Soft Computing in the Conception, Design and Deployment of Intelligent Systems , 1997, Software Agents and Soft Computing.

[18]  M. Karplus,et al.  Genetic neural networks for quantitative structure-activity relationships: improvements and application of benzodiazepine affinity for benzodiazepine/GABAA receptors. , 1996, Journal of medicinal chemistry.

[19]  F. Burden.  Using Artificial Neural Networks to Predict Biological Activity from Simple Molecular Structural Considerations , 1996 .

[20]  D. Rouvray.  Fuzzy Logic in Chemistry , 1997 .

[21]  Min Xiao,et al.  Artificial Neural Networks Applied to Classification of Mutagenic Activity of Nitro-substituted Polycyclic Aromatic Hydrocarbons , 1994, Comput. Chem..

[22]  Gareth Jones,et al.  A genetic algorithm for flexible molecular overlay and pharmacophore elucidation , 1995, J. Comput. Aided Mol. Des..

[23]  J Moult,et al.  Genetic algorithms for protein structure prediction. , 1996, Current opinion in structural biology.

[24]  Maurice Chastrette,et al.  Structure-Odor Relationships: Using Neural Networks in the Estimation of Camphoraceous or Fruity Odors and Olfactory Thresholds of Aliphatic Alcohols , 1996, J. Chem. Inf. Comput. Sci..

[25]  César Hervás-Martínez,et al.  Estimation of Parameters of Kinetic Compartmental Models by Use of Computational Neural Networks , 1997, J. Chem. Inf. Comput. Sci..

[26]  Jure Zupan,et al.  Application of a Feed-Forward Artificial Neural Network as a Mapping Device , 1997, J. Chem. Inf. Comput. Sci..

[27]  Igor V. Tetko,et al.  Neural Network Studies, 2. Variable Selection , 1996, J. Chem. Inf. Comput. Sci..

[28]  Lemont B. Kier,et al.  A Cellular Automata Model of Oil-Water Partitioning , 1995, J. Chem. Inf. Comput. Sci..

[29]  J. Taskinen,et al.  Neural network modeling for estimation of the aqueous solubility of structurally related drugs. , 1997, Journal of pharmaceutical sciences.

[30]  Barry Robson,et al.  PRO_LIGAND: An approach to de novo molecular design. 3. A genetic algorithm for structure refinement , 1995, J. Comput. Aided Mol. Des..

[31]  Hugo Kubinyi,et al.  Evolutionary variable selection in regression and PLS analyses , 1996 .

[32]  D. Farin,et al.  Use of fractal geometry to determine effects of surface morphology on drug dissolution. , 1992, Journal of pharmaceutical sciences.

[33]  A Garfinkel,et al.  Controlling cardiac chaos. , 1992, Science.

[34]  Anton J. Hopfinger,et al.  Application of Genetic Function Approximation to Quantitative Structure-Activity Relationships and Quantitative Structure-Property Relationships , 1994, J. Chem. Inf. Comput. Sci..

[35]  Larry S. Liebovitch,et al.  Using fractals to understand the opening and closing of ion channels , 2006, Annals of Biomedical Engineering.

[36]  Jaroslaw Polanski,et al.  The Receptor-like Neural Network for Modeling Corticosteroid and Testosterone Binding Globulins , 1997, J. Chem. Inf. Comput. Sci..

[37]  K. Shulman,et al.  Fuzzy logic pharmacokinetic modeling: Application to lithium concentration prediction , 1997, Clinical pharmacology and therapeutics.

[38]  Lemont B. Kier,et al.  Simulation of First-Order Chemical Kinetics Using Cellular Automata , 1997, J. Chem. Inf. Comput. Sci..

[39]  Lutgarde M. C. Buydens,et al.  Parallel Processing of Chemical Information in a Local Area Network - II. a Parallel Cross-validation Procedure for Artificial Neural Networks , 1996, Comput. Chem..

[40]  Dmitri B. Kireev,et al.  ChemNet: A Novel Neural Network Based Method for Graph/Property Mapping , 1995, J. Chem. Inf. Comput. Sci..

[41]  Lemont B. Kier,et al.  A Cellular Automata Model of an Aqueous Solution , 1994, J. Chem. Inf. Comput. Sci..

[42]  Marjan Vracko,et al.  A Study of Structure-Carcinogenic Potency Relationship with Artificial Neural Networks. The Using of Descriptors Related to Geometrical and Electronic Structures , 1997, J. Chem. Inf. Comput. Sci..

[43]  J A Koziol,et al.  Prediction of binding to MHC class I molecules. , 1995, Journal of immunological methods.

[44]  C. Washington,et al.  Fractal morphology of drug aggregates in aerosol propellant suspensions , 1995 .

[45]  Larry S. Liebovitch,et al.  A model of ion channel kinetics based on deterministic, chaotic motion in a potential with two local minima , 2006, Annals of Biomedical Engineering.

[46]  Marjana Novic,et al.  Quantitative Structure-Activity Relationship of Flavonoid p56lck Protein Tyrosine Kinase Inhibitors. A Neural Network Approach , 1997, J. Chem. Inf. Comput. Sci..

[47]  Jaroslaw Polanski,et al.  Neural Nets for the Simulation of Molecular Recognition within MS-Windows Environment , 1996, J. Chem. Inf. Comput. Sci..

[48]  J Brickmann,et al.  Segmentation of protein surfaces using fuzzy logic. , 1994, Journal of molecular graphics.

[49]  Y. Martin,et al.  Designing combinatorial library mixtures using a genetic algorithm. , 1997, Journal of medicinal chemistry.

[50]  Wayne J. Pullan,et al.  Structure Prediction of Benzene Clusters Using a Genetic Algorithm , 1997, J. Chem. Inf. Comput. Sci..

[51]  D. Maddalena,et al.  Prediction of receptor properties and binding affinity of ligands to benzodiazepine/GABAA receptors using artificial neural networks. , 1995, Journal of medicinal chemistry.

[52]  Kwok Ching Tsui,et al.  An Introduction to Soft Computing - A Tool for Building Intelligent Systems , 1997, Software Agents and Soft Computing.

[53]  Morton E. Munk,et al.  The Neural Network as a Tool for Multispectral Interpretation , 1996, J. Chem. Inf. Comput. Sci..

[54]  Umpei Nagashima,et al.  Development of Neural Network Simulator for Structure-Activity Correlation of Molecules (NECO). Prediction of Endo/Exo Substitution of Norbornane Derivatives and of Carcinogenic Activity of PAHs from 13C-NMR Shifts , 1996, J. Chem. Inf. Comput. Sci..

[55]  Jonathan A. Ellman,et al.  Synthesis and Applications of Small Molecule Libraries. , 1996, Chemical reviews.

[56]  G B Ermentrout,et al.  Cellular automata approaches to biological modeling. , 1993, Journal of theoretical biology.

[57]  Desmond J. Maddalena.  Review Biologicals & Immunologicals: Applications of artificial neural networks to quantitative structure-activity relationships , 1996 .

[58]  G Reibnegger,et al.  Neural networks as a tool for compact representation of ab initio molecular potential energy surfaces. , 1996, Journal of Molecular Graphics.

[59]  P. Mezey,et al.  Fuzzy molecular fragments in drug research , 1997 .

[60]  Metin Akay,et al.  Fuzzy sets in life sciences , 1997, Fuzzy Sets Syst..

[61]  Barry M. Wise,et al.  A comparison of neural networks, non-linear biased regression and a genetic algorithm for dynamic model identification , 1995 .

[62]  J Brickmann,et al.  Self similarity of protein surfaces. , 1992, Biophysical journal.

[63]  D J Livingstone,et al.  Novel method for the display of multivariate data using neural networks. , 1991, Journal of molecular graphics.

[64]  P. Willett.  Genetic algorithms in molecular recognition and design. , 1995, Trends in biotechnology.

[65]  Daniel Cabrol-Bass,et al.  Identification of Structural Features from Mass Spectrometry Using a Neural Network Approach: Application to Trimethylsilyl Derivatives Used for Medical Diagnosis , 1996, J. Chem. Inf. Comput. Sci..

[66]  Thomas R. Cundari,et al.  A Comparison of Neural Networks versus Quantum Mechanics for Inorganic Systems , 1997, J. Chem. Inf. Comput. Sci..

[67]  Johann Gasteiger,et al.  The comparison of geometric and electronic properties of molecular surfaces by neural networks: Application to the analysis of corticosteroid-binding globulin activity of steroids , 1996, J. Comput. Aided Mol. Des..

[68]  J. T. Carstensen,et al.  The Use of Fractal Geometry in Pharmaceutical Systems , 1993 .

[69]  Hiroshi Yoshida,et al.  Optimization of the Inner Relation Function of QPLS Using Genetic Algorithm , 1997, J. Chem. Inf. Comput. Sci..

[70]  Frank R. Burden,et al.  Mapping Analytic Functions Using Neural Networks , 1994, J. Chem. Inf. Comput. Sci..

[71]  Daniel Svozil,et al.  Neural Network Prediction of the Solvatochromic Polarity/Polarizability Parameter PiH2[S_EL2;quad] , 1997, J. Chem. Inf. Comput. Sci..