Bayesian neural nets for modeling in drug discovery

Abstract Bayesian regularized artificial neural networks (BRANNs) are used in the development of quantitative SAR models. These networks have the potential to solve several problems that arise in QSAR modeling such as choice of model, robustness of model, choice of validation set, size of validation effort, and optimization of network architecture. The application of the methods to a wide range of problems, including target-based QSAR, ADMET modeling and eukaryotic promoter finding, is illustrated.

[1]  G Beck,et al.  Evaluation of human intestinal absorption data and subsequent derivation of a quantitative structure-activity relationship (QSAR) with the Abraham descriptors. , 2001, Journal of pharmaceutical sciences.

[2]  Yi Li,et al.  In silico ADME/Tox: why models fail , 2003, J. Comput. Aided Mol. Des..

[3]  David Mackay,et al.  Probable networks and plausible predictions - a review of practical Bayesian methods for supervised neural networks , 1995 .

[4]  R. Cramer,et al.  Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. , 1988, Journal of the American Chemical Society.

[5]  Lemont B. Kier,et al.  Modeling Blood-Brain Barrier Partitioning Using the Electrotopological State , 2002, J. Chem. Inf. Comput. Sci..

[6]  Frank R. Burden,et al.  Use of Automatic Relevance Determination in QSAR Studies Using Bayesian Neural Networks , 2000, J. Chem. Inf. Comput. Sci..

[7]  S. Teague Implications of protein flexibility for drug discovery , 2003, Nature Reviews Drug Discovery.

[8]  Peter Wolschann,et al.  Bayesian Neural Networks for Aroma Classification , 2002, J. Chem. Inf. Comput. Sci..

[9]  Frank R. Burden,et al.  Atomistic topological indices applied to benzodiazepines using various regression methods , 1998 .

[10]  C. Hansch,et al.  p-σ-π Analysis. A Method for the Correlation of Biological Activity and Chemical Structure , 1964 .

[11]  M. Randic Characterization of molecular branching , 1975 .

[12]  Pier Luigi Luisi,et al.  Emergence in Chemistry: Chemistry as the Embodiment of Emergence , 2002 .

[13]  David A Winkler,et al.  Application of neural networks to large dataset QSAR, virtual screening, and library design. , 2002, Methods in molecular biology.

[14]  Martin Karplus,et al.  Molecular dynamics simulations of biomolecules. , 2002, Nature structural biology.

[15]  David A. Winkler,et al.  The role of quantitative structure-activity relationships (QSAR) in biomolecular discovery , 2002, Briefings Bioinform..

[16]  Mohammad Bagher Menhaj,et al.  Training feedforward networks with the Marquardt algorithm , 1994, IEEE Trans. Neural Networks.

[17]  H. van de Waterbeemd,et al.  ADMET in silico modelling: towards prediction paradise? , 2003, Nature reviews. Drug discovery.

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

[19]  Johann Gasteiger,et al.  Neural networks in chemistry and drug design , 1999 .

[20]  Philipp Bucher,et al.  The Eukaryotic Promoter Database EPD , 1998, Nucleic Acids Res..

[21]  B. Testa,et al.  Molecules as complex adaptative systems: constrained molecular properties and their biochemical significance. , 2000, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.

[22]  Wray L. Buntine,et al.  Bayesian Back-Propagation , 1991, Complex Syst..

[23]  F. Burden,et al.  Robust QSAR models using Bayesian regularized neural networks. , 1999, Journal of medicinal chemistry.

[24]  Vladimir B. Bajic,et al.  Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters , 2002, Bioinform..

[25]  Paul A. Smith,et al.  Comparison of Linear and Nonlinear Classification Algorithms for the Prediction of Drug and Chemical Metabolism by Human UDP-Glucuronosyltransferase Isoforms , 2003, J. Chem. Inf. Comput. Sci..

[26]  Vladimir Brusic,et al.  MHCPEP, a database of MHC-binding peptides: update 1996 , 1997, Nucleic Acids Res..

[27]  J M Scherrmann,et al.  Drug delivery to brain via the blood-brain barrier. , 2002, Vascular pharmacology.

[28]  Pierre Bruneau,et al.  Search for Predictive Generic Model of Aqueous Solubility Using Bayesian Neural Nets , 2001, J. Chem. Inf. Comput. Sci..

[29]  David J. C. MacKay,et al.  Bayesian Interpolation , 1992, Neural Computation.