Review articles

Monday-Tuesday, June 28-29

Microarray Analysis

Overview of the Alliance for Cellular Signalling, Nature 420, 703-706 (2002)
The use and analysis of microarray data, A. Butte, Nature Reviews: Drug Discovery 1, 951-960 (2002)
Microarray Expression profiling identifies genes with altered expression in HDL-Deficient Mice, M.J. Callow et al., Genome Research 10, 2022-2029 (2000)
Cluster analysis and display of genome-wide expression patterns, M.B. Eisen et al., Genetics 95, 14863-14868 (1998)
A new web-based data mining tool for the identification of candidate genes for human genetic disorders, M.A. van Driel et al., European Journal of Human Genetics 11, 57-63 (2003)
Better therapeutics through microarrays, D.L. Gerhold et al., Nature Genetics Suppl. 32, 547-552 (2002)
DNA microarrays in drug discovery and development, C. Debouck, P.N. Goodfellow, Nature Genetics Suppl. 21, 48-50 (1999)
From patterns to pathways: gene expression data analysis comes of age, D.K. Slonim, Nature Genetics Suppl. 32, 502-508 (2002)
Biomedical Discovery with DNA Arrays, R.A. Young, J.A. McCammon, Cell 102, 9-15 (2000)

Wednesday, June 30

Homology Modelling

Homology Modeling, Elmar Krieger, in: P.E. Bourne and H. Weissig (Eds.), Structural Bioinformatics, p. 507-521 (Wiley-Liss, 2003)
Structural Quality Assurance, R.A. Laskowski, in: P.E. Bourne and H. Weissig (Eds.), Structural Bioinformatics, p. 271-301 (Wiley-Liss, 2003)

Thursday, July 1

Nuclear Receptors

Nuclear receptor ligand-binding domains: three-dimensional structures, molecular interactions and pharmacological implications, W. Bourguet, P. Germain, H. Gronemeyer, Trends Pharmacol. Sci. 21, 381-388 (2000)
The nuclear receptor ligand-binding domain: structure and function, D. Moras, H. Gronemeyer, Current Opinion in Cell Biology 10, 384 (1998)
Nuclear Receptor Signaling Atlas
Nuclear Receptor Online Journal

Docking and Virtual screening

Small Molecule Docking and Scoring, I. Muegge, M. Rarey, Reviews in Computational Chemistry 17, 1-60 (2001)
The Use of Scoring Functions in Drug Discovery Application, H.J. Böhm, M. Stahl, Reviews in Computational Chemistry 18, 41-87 (2002)
The performance of current methods in ligand-protein docking, B.J. McConkey, V. Sobolev, M. Edelman, Current Science 83, 845 (2002)
Integration of virtual and high-throughput screening, J. Bajorath, Nature Reviews: Drug Discovery 1, 882 (2202)
Chemical database techniques in drug discovery, M.A. Miller, Nature Reviews: Drug Discovery 1, 227 (2002)
Large-scale virtual screening for discovering leads in the postgenomic era, B. Waszkowycz, T.D.J. Perkins, R.A. Sykes, J. Li, IBM systems journal 40, 360 (2001)

Friday, July 2

2D, 3D

Strategies for the determination of pharmacophoric 3D database queries, J.H. van Drie, Journal of Computer-Aided Molecular Design 11, 39 (1997)
A pharmacophore model for dopamine D4 receptor antagonists, J. Böstrom, K. Gundertofte, T. Lijefors Journal of Computer-Aided Molecular Design 14, 769 (2000)
3D Pharmacophore Searching, K. Davies, R. Upton, Network Science

Monday, July 5

QSAR and CoMFA

Introduction to QSAR and Drug Design, D. Bevan (1996)
Introduction to QSAR Methodology, A.B. Richon and S.S. Young (1997)
QSAR and 3D QSAR in Drug Design, Part 1: methodology, H. Kubinyi, in: Drug Discovery Today 2, 457-467 (1997)
QSAR and 3D QSAR in Drug Design, Part 2: applications and problems, H. Kubinyi, in: Drug Discovery Today 2, 538-546 (1997)
Comparative Molecular Field Analysis (CoMFA), H. Kubinyi, in: J. Gasteiger (Ed.), Encyclopedia of Computational Chemistry (Wiley, London, 1998)
CoMFA: A Field of Dreams? S. Semus (1996)
QSAR Models for Binding of Estrogenic Compounds to Estrogen Receptor α and β Subtypes, W. Tong et al., Endocrinology 138, 4022-4025 (1997)
QSAR Models Using a Large Diverse Set of Estrogens, L.M. Shi et al., J. Chem. Inf. Comput. Sci. 41, 186-195 (2001)
Comparative Molecular Field Analysis of Substrates for an Aryl Sulfotransferase Based on Catalytic Mechanism and Protein Homology Modeling, V. Sharma and M.W. Duffel, J. Med. Chem. 45, 5514-5522 (2002)

Molecular Dynamics

Molecular dynamics simulations, Th. Hansson, C. Oostenbrink, W.F. van Gunsteren, Structural Biology 12, 190-196 (2002)
Molecular dynamics simulations of biomolecules, M. Karplus, J.A. McCammon, Nature Structural Biology 9, 646-652, 788 (2002)
Computer Simulation of Molecular Dynamics; Methodology, Applications, and Perspectives in Chemistry, W.F. van Gunsteren, H.J.C. Berendsen, Angew. Chem. Int. Ed. Engl. 29, 992-1023 (1990) (Only hard copy available)

Tuesday, July 6

ADME-TOX

ADMET in silico modelling: towards prediction paradise? H. v.d. Waterbeemd, E. Gifford, Nature Reviews Drug Discovery 2, 192-204 (2003)
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings C. Lipinski, F. Lombardo, B.W. Dominy, P.J. Feeney,Advanced drug delivery reviews 23, 3-25 (1997)

Only hard copy available:

Current Topics in Medicinal Chemistry: ADMET Informatics: Adding Innovation to Structure Based Drug Design, Editor: R. Bursi, Volume 3, Number 11, 2003, Bentham Science Publishers LTD.

QM in Drug Design

Applications of Quantum Chemical Methods in Drug Design H. D. Höltje, M. Höltje, Unpublished.

Wednesday, July 7

Additional papers for the exam.

Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of Anti-SARS Drugs, K. Anand, J. Ziebuhr, P. Wadhwani, J.R. Mesters, R. Hilgenfeld, Science 300, 1763-1767 (2003)
Hit and Lead Generation: Beyond High-Throughput Screening, K.H. Bleicher, H.J. Böhm, K. Müller and A.I. Alanine, Nature Reviews: Drug Discovery 2, 360-378 (2003)
Implications of Protein Flexibility for Drug Discovery Simon J. Taegue, Nature Reviews: Drug Discovery 2, 527-541 (2003)