Structural Bioinformatics Tools for Drug Design

Structural Bioinformatics Tools for Drug Design Extraction of Biologically Relevant Information from Structural Databases Exercises for the book Structural Bioinformatics Tools for Drug Design: Extraction of Biologically Relevant Information from Structural Databases from authors: Koča, J., Svobodová Vařeková, R., Pravda, L., Berka, K., Geidl, S., Sehnal, D., Otyepka, M.

Exercises for Chapter 3 - Structural Bioinformatics Databases of General Use

  1. Use of PDBe
  2. Use of RCSB and ChEMBL
  3. Use of PDBsum
  4. Use of CATH
 

Exercises for Chapter 4 - Validation

  1. Detecting of problematic ligands in nipah G attachment glycoprotein
  2. Validation of sucrose (SUC) in Plant Photosystem I – missing atoms
  3. Validation of β-carotene (BCR) in Plant Photosystem I – missing rings
  4. Validation of maltose (MAL) ligands in Protein Data Bank – missing atoms and rings
  5. Detection of atom substitution in biotin (BTN) from 50S Complex (PDB ID 1kqs)
  6. Detection of chirality problems in all sialic acids (SIA) from Protein Data Bank
  7. Detection of chirality problems in testosterone derivatives
  8. Obtaining of structure validation data for a rhodostomin
  9. Obtaining of structure validation data for a mutant of cytochrome P450cam
  10. Understanding of PDB validation reports summary criteria for oxy-hemoglobine in methanol

Exercises for Chapter 6 - Detection of Channels

  1. Gramicidin D channel
  2. ProbeRadius and InteriorThreshold settings for channel identification
  3. Channel starting point
  4. Polyamine oxidase binding channel
  5. Polypeptide channel in ribosome

Exercises for Chapter 7 - Characterization via Charges

  1. Detection of the first dissociating hydrogen in 3-hydroxy benzoic acid
  2. Comparison of charges in phenol molecules and detection of correlation between charges and pKa.
  3. Comparison of charge distributions in cocaine binding sites
  4. Comparison of a charge distribution in activated and inhibited apoptotic proteins

Exercises for Chapter 8 - Channel Characteristics

  1. Gramicidin D pore
  2. Channels in Cytochrome P450 3A4
  3. Substrate tunnel
  4. Importance of Bottleneck

Exercises for Chapter 9 - Complete Process of Data Extraction and Analysis

  1. Lectin example (Validation, extraction, comparison, charge calculation)
  2. Cytochrome P450 example (Database search, detection of channels, channel characterization)