AMIDD (2022) Lecture 6: Offline activities
Dear participants of the AMIDD 2022 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.

And instead of one week, you have TWO weeks to finish the tasks (by November 11th).

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,
David
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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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