QSAR World - Literature - Recommended Reading

CoMFA and CoMSIA 3D-QSAR analysis on hydroxamic acid derivatives as urease inhibitors

Zaheer -ul-Haq, Abdul Wadood and Reaz Uddin

Journal of Enzyme Inhibition and Medicinal Chemistry, 2008. Get Paper

Receptor-Based Modeling and 3D-QSAR for a Quantitative Production of the Butyrylcholinesterase Inhibitors Based on Genetic Algorithm

Zaheer-ul-Haq,*,†,§ Reaz Uddin,‡,§ Hongbin Yuan, Pavel A. Petukhov, M. Iqbal Choudhary,§ and Jeffry D. Madura⊥

J. Chem. Inf. Model. 2008, 48, 1092–1103 Get Paper

Building a BioChemformatics Database

Jan H. Jensen*†, Thomas Hoeg-Jensen‡ and Søren B. Padkjær§

J. Chem. Inf. Model., Article ASAP, Publication Date (Web): November 21, 2008 Get paper

Similarity Searching Using Fingerprints of Molecular Fragments Involved in Protein−Ligand Interactions

Lu Tan, Eugen Lounkine and Jürgen Bajorath*

J. Chem. Inf. Model., Article ASAP, Publication Date (Web): November 13, 2008 Get paper

Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language

Nico Adams*†, Jerry Winter‡, Peter Murray-Rust† and Henry S. Rzepa§

J. Chem. Inf. Model., 2008, 48 (11), pp 2118–2128, Publication Date (Web): November 8, 2008 Get paper

The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery

Johannes Kirchmair†‡, Patrick Markt†, Simona Distinto†§, Daniela Schuster†, Gudrun M. Spitzer∥, Klaus R. Liedl∥, Thierry Langer⊥ and Gerhard Wolber*†‡

J. Med. Chem., 2008, 51 (22), pp 7021–7040, Publication Date (Web): November 1, 2008 Get paper

Proteomics, networks and connectivity indices

González-Díaz H, González-Díaz Y, Santana L, Ubeira FM, Uriarte E.

Proteomics. 2008 Feb;8(4):750-78. Review Get paper

Medicinal chemistry and bioinformatics--current trends in drugs discovery with networks topological indices.

González-Díaz H, Vilar S, Santana L, Uriarte E.

Curr Top Med Chem. 2007;7(10):1015-29. Review Get paper

Recent advances in QSAR and their applications in predicting the activities of chemical molecules, peptides and proteins for drug design.

Du QS, Huang RB, Chou KC.

JCurr Protein Pept Sci. 2008 Jun;9(3):248-60 Get Paper

Physics and chemistry-driven artificial neural network for predicting bioactivity of peptides and proteins and their design.

Huang RB, Du QS, Wei YT, Pang ZW, Wei H, Chou KC

J Theor Biol. 2008 Sep 17. [Epub ahead of print] Get Paper

Approaches to Measure Chemical Similarity - a review

Nina Nikolova and Joanna Jaworska

QSAR Comb. Sci., 22 (9-10), 1006-1026, 2003. Get Paper

A Classification and Regression Tool for Compound Classification and QSAR Modeling

Vladimir Svetnik, Andy Liaw, Christopher Tong, J. Christopher Culberson, Robert P. Sheridan, and Bradley P. Feuston

J. Chem. Inf. Comput. Sci., 43(6), 1947-1958, 2003.Get Paper

Robust Cross-Validation of Linear Regression QSAR Models

Dmitry A. Konovalov*†, Lyndon E. Llewellyn‡, Yvan Vander Heyden§ and Danny Coomans†

J. Chem. Inf. Model., 2008, 48 (10), pp 2081–2094

DOI: 10.1021/ci800209k, Publication Date (Web): October 1, 2008 Get Paper

External Validation and Prediction Employing the Predictive Squared Correlation Coefficient  Test Set Activity Mean vs Training Set Activity Mean

Gerrit Schüürmann*†‡, Ralf-Uwe Ebert†, Jingwen Chen§, Bin Wang§ and Ralph Kühne†

J. Chem. Inf. Model., 2008, 48 (11), pp 2140–2145, Publication Date (Web): October 28, 2008, Get Paper

Principles of QSAR models validation: internal and external

Paola Gramatica

QSAR Comb.Sci. 2007, 26(5), 694-701. DOI: 10.1002/qsar.200610151 Get Paper

The Trouble with QSAR (or How I Learned To Stop Worrying and Embrace Fallacy)

Johnson, S.R.

J. Chem. Inf. Model., 48, 1, 25 - 26, 2008, 10.1021/ci700332k Get Paper

Beware of q2!

Alexander Golbraikh, Alexander Tropsha

Journal of Molecular Graphics and Modelling, Volume 20, Issue 4, , January 2002, Pages 269-276 Get Paper

The Importance of Being Earnest: Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models

Alexander Tropsha, Paola Gramatica, and Vijay K. Gombar

QSAR Comb. Sci., 22 (1), 69-77, 2003. Get Paper

Methods for reliability and uncertainty assessment and for applicability evaluations of classification- and regression-based QSARs

Lennart Eriksson, Joanna Jaworska, Andrew P Worth, Mark T D Cronin, Robert M McDowell, and Paola Gramatica

Environ Health Perspect.,111(10): 1361-1375, 2003. Get Paper

Expert Opinion on Drug Metabolism & Toxicology

Kalyanasundaram "Kas" Subramanian

Expert Opinion on Drug Metabolism & Toxicology October 2005, Vol. 1, No. 3, Pages 555-564 (doi: 10.1517/17425255.1.3.555). Get Paper

For a complematary hard copy of this paper please contact edi...@qsarworld.com

ADMET In Silico Modelling: Towards Prediction Paradise?

Han van de Waterbeemd and Gifford

Nature Reviews Drug Dicovery, 2, 192-204, 2003. Get Paper

In Silico ADME Prediction: Data, Models, Facts and Myths.

Lombardo, F.; Gifford, E.; Shalaeva, M. Y.

Mini Reviews in Medicinal Chemistry, 3, 861-875, 2003

ADMET-turning chemicals into drugs

John Hodgson

Nature Biotechnology, 19, 722 - 726, 2001. Get Paper

Drug-like properties and the causes of poor solubility and poor permeability

Lipinski, C.A.,

Journal of Pharmacological and Toxicological Methods, 44, 235-249, 2000.

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

Lipinski, C.A.; Lombardo, F.; Dominy, B.W.; Feeney, P.J.

Adv Drug Deliv Rev., 23, 3-25, 1997.

Managing the drug discovery/ development interface.

Kennedy T.

DDT, 2, 436-444, 1997.

Chemical Descriptors Library (CDL): A Generic, Open Source Software Library for Chemical Informatics

Sykora, Vladimir J. and Leahy, David E.

J. Chem. Inf. Model., 2008, 10.1021/ci800135h Get Paper

The Characterization of Chemical Structures Using Molecular Properties - A Survey

David J. Livingstone

J. Chem. Inf. Comput. Sci., 40, 195-209, 2000. Get Paper

Drug Discovery: A Historical Perspective

Jurgen Drews

Science, 287, 1960-1964, 2000. Get Paper

Outlier Detection in Multivariate Analytical Chemical Data

William J. Egan and Stephen L. Morgan

Anal. Chem., 70 (11), 2372 -2379, 1998. Get Paper

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