Jaroslav Koča & Radka Svobodová Vařeková 
Structural Bioinformatics Tools for Drug Design [PDF ebook] 
Extraction of Biologically Relevant Information from Structural Databases

1. Introduction.- 2. Biomacromolecular fragments .- 3. Databases.- 4. Detection & Extraction.- a. Biomacromolecular fragments and structural patterns.- b. channels and pores.- 5. Validation.- 6. Characterization.- a. Partial atomic charges.- b. Channel characteristics.- 7. Selected Examples.

Prof. RNDr. Jaroslav Koca, Dr Sc., is director of the Central European Institute of Technology and Head of the research group Computational Chemistry at Masaryk University in Brno, Czech Republic.
His field of expertise is mathematical and computer assisted chemistry and biochemistry, computer assisted molecular modeling of biologically interesting chemical species, information technology in chemistry, biochemistry, and environmental chemistry. Last years´ projects were mainly on conformational search, molecular docking and molecular dynamics simulations on peptides, proteins, oligonucleotides, nucleotide sugars, and carbohydrates. Methods for analysis conformational potential energy surfaces and energy landscapes of chemical reactions using molecular mechanics and quantum chemistry techniques. For more information see: http://www.chemi.muni.cz/~jkoca/