Q2. What are the main factors influencing the robustness of interactome results?
Sampling bias, missing interactions and false positives are all important factors influencing the robustness of interactome results.
Q3. What is the main reason for the difficulty in designing drugs for a group of targets?
designing drugs for a group of targets with similar binding sites is challenging due to low specificity as exemplified by the drug design efforts against the ATP binding sites of protein kinases.
Q4. What is the important factor to improve the productivity of the pharmaceutical industry?
Improving the quality of target selection is widely considered as the single most important factor to improve the productivity of the pharmaceutical industry.
Q5. What are the widely used datasets to characterize disease-associated proteins?
mRNA expression patterns, genome-wide association studies (GWAS) of disease-associated single-nucleotide polymorphisms (SNPs) and disease-related changes in posttranslational modifications (such as the phospho-proteome) are just three of the most widely used datasets, which may also include system-wide changes of subcellular localization.
Q6. What is the role of the polar fragments in the prediction of bioavailability?
The identification of polar ‘emphatic’ fragments anchoring chemicals to serum albumin and hydrophobic fragments determining albumin binding was an important step in network-related prediction of bioavailability.
Q7. What is the importance of the description of protein structure and dynamics?
Proteins are the major targets of drug action, and therefore the description of their structure and dynamics has a crucial importance in the determination of drug binding sites, as well as in prediction of drug effects at the sub-molecular level.
Q8. What is the important measure of network essentiality?
The number of neighbors in protein–protein interaction networks is an important network measure of essentiality (Jeong et al., 2001).
Q9. What are the major health challenges that are in desperate need of new medicines?
Some of the major health challenges, such as many types of cancers and infectious diseases, diabetes and neurodegenerative diseases are in desperate need of innovative medicines.
Q10. What is the important application of QSAR-related similarity networks?
Another important application of QSAR-related similarity networks is the molecular fragment network of human serum albumin binding defined by Estrada et al. (2006).
Q11. What is the effect of inhibitors of a specific cancer hallmark?
when inhibitors of a specific cancer hallmark are used separately, they may even strengthen another hallmark, like certain types of angiogenesis inhibitors increased the rate of metastasis.
Q12. What is the common way to construct protein binding site similarity networks?
• Protein binding site similarity networks may be constructed using a simplified representation of binding sites as geometric patterns, or numerical fingerprints.
Q13. What is the definition of the substrate-envelope for HIV reverse transcriptase?
Tuske et al. (2004) defined the substrate-envelope for HIV reverse transcriptase as the space occupied by various conformations of naturally occurring ligands and their targets.
Q14. What are the main factors that determine the applicability of network analysis in drug design?
The applicability of network analysis in drug design is determined by the following major factors: 1.) proper definition of network nodes, edges and edge weights; 2.) data quality and carefully defined, uniformly applied data inclusion criteria; 3.) data refinement by genetic variability, aging, environmental effects and compounding pathologies such as bacterial or viral infections (Arrell & Terzic, 2010; Kolodkin et al., 2012).
Q15. What is the way to find a set of indirect targets?
Target sets, which are highly relevant at the systems-level, but have diverse binding site structures may require the identification of a set of indirect targets selectively influencing the desired target set, but posing a more feasible lead development task.
Q16. How many core modules of the human interactome were affected by mRNA changes?
Suthram et al. (2010) identified 59 core modules out of the 4620 modules of the human interactome, which were affected by mRNA changes in more than half of the 54 diseases examined.
Q17. How many modules of the human interactome are dysregulated?
Suthram et al. (2010) identified 59 modules out of the 4620 modules of the human interactome, which are dysregulated in at least half of the 54 diseases tested, and were enriched in known drug targets.
Q18. What is the fruitful basis for the discovery of a new drug?
As the pharmacologist and Nobel Laureate James Black said: “themost fruitful basis for the discovery of a new drug is to start with an old drug” (Chong & Sullivan,2007).