Table of Contents

Preface vii

Combination of molecular similarity measures using data fusion 1

Optimization of the drug-likeness of chemical libraries 17

J. Sadowski

Generating consistent sets of thermodynamic and structural data for analysis of protein-ligand interactions 29

Multiple molecular superpositioning as an effective tool for virtual database screening 43

C. Lemmen, M. Zimmermann and T. Lengauer

A recursive algorithm for efficient combinatorial library docking 63

M. Rarey and T. Lengauer

Modifications of the scoring function in FlexX for virtual screening applications 83

M. Stahl

A knowledge-based scoring function for protein-ligand interactions: Probing the reference state 99

I. Muegge

Predicting binding modes, binding affinities and 'hot spots' for protein-ligand complexes using a knowledge-based scoring function 115

H. Gohlke, M. Hendlich and G. Klebe

Hydrophobicity maps and docking of molecular fragments with solvation 145

N. Majeux, M. Scarsi, C. Tenette-Souaille and A. Caflisch

Virtual screening with solvation and ligand-induced complementarity 171

V. Schnecke and L.A. Kuhn

Similarity versus docking in 3D virtual screening 191

J. Mestres and R.M.A. Knegtel

Discovering high-affinity ligands from the computationally predicted structures and affinities of small molecules bound to a target: A virtual screening approach 209

In vitro and in silico affinity fingerprints: Finding similarities beyond structural classes 231

H. Briem and U.F. Lessel

Computer-assisted synthesis and reaction planning in combinatorial chemistry 245

J. Gasteiger, M. Pförtner, M. Sitzmann, R. Höllering, O. Sacher, T. Kostka and N. Karg

Evaluation of reactant-based and product-based approaches to the design of combinatorial libraries 265

V.J. Gillet and O. Nicolotti

Author Index Subject Index

289 291

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