AMIDD (2023) Lecture 9: Offline activities
Dear participants of the AMIDD 2023 course,

Please find below the form to collect your answers to the questions about the review paper *Computational Methods in Drug Discovery* by Sliwoski.

The paper focuses mostly on computational methods in structure-based and ligand-based computer-aided drug design (CADD). It is, despite being well written, very long (62 pages). Therefore, please try to get **high-level** understanding, instead of diving into each detail, by following the questions below.

The aim of the activity is to give you a comprehensive impression of computational methods in drug design. I will try to address issues that are particularly confusing, and questions that are challenging or interesting for many of you in due course.

Best regards,
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Q1. What is the method commonly used to benchmark performance of different techniques of computer-aided drug design (CADD)? (page 342, left column)
Q2: what do we mean by molecular dynamics? (page 346)
Q3: what are the three basic methods to represent target and ligand structures in silico? (p 347)
Q4: what sampling algorithms are there for protein-ligand docking? (p347-350) Can you explain one of them using your words?
Q5: what are the key steps in structure-based virtual high-throughput screenings (SB-vHTS)? (p351)
Q6: What is the usual starting point of structure-based CADD campaign? (p356, left column)
Q7: what do we mean by 'pharmacophore'? (p357, p375 left column)
Q8: In QSAR analysis, why it is important to select optimal descriptors/features? (p374, right column)
Q9: What do we mean by the acronyms DMPK and ADMET? (p379)
Q10: why common CADD methods have difficulties handling protein-protein interaction and protein-DNA interactions? (p386, right column)
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