Biomolecular Modelling - Bewerkingsoverzicht

R0837419: /* Examenvragen */

2025-01-14T13:44:05Z

Examenvragen

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	== Examenvragen ==		== Examenvragen ==
			'''Exam of 13/01/2025'''

			1. You have the structure of a receptor and a few active ligands that inhibit a receptor. There is no structure of the complex. The ligands inhibit the receptor but can not be used as drug. There is a database of drug-like compounds which you need to computationally scan to find active ligands. Which methods could you use and how do they work? Explain why these compounds can not be used as drug? Include ROC and enhancement in your answer. (15)

			2. 15 multiple choice questions about the entire course. There was one question for each of the papers. (15)

			3. The main differences and similarities between genetic algorithms and monte carlo simulated annealing. (10)

			4. Describe the steps of molecular dynamics. (10)

	'''Exam of 15/01/2024'''		'''Exam of 15/01/2024'''

R0792390: /* Examenvragen */

2025-01-13T16:14:56Z

Examenvragen

← Oudere versie		Versie van 13 jan 2025 18:14
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	== Examenvragen ==		== Examenvragen ==

	~~'''Exam of 13/01/2025, Afternoon'''~~
	~~No oral question since professor couldn't be present during all exam moments.~~

	1. You have the structure of a receptor and a few active ligands that inhibit a receptor. There is a structure of the complex. The ligands inhibit the receptor but can not be used as drug. There is a database of drug-like compounds which you need to computationally scan to find active ligands. Which methods could you use and how do they work? Why can't the compounds be optimized further?

	~~2. 15 multiple choice questions the entire course. There was one question for each of the papers. (15)~~

	~~3. The main differences and similarities between genetic algorithms and monte carlo simulated annealing. (10)~~

	~~4. Explain the steps of a molecular dynamics simulation. (10)~~

	'''Exam of 15/01/2024'''		'''Exam of 15/01/2024'''

R0792390: /* Examenvragen */

2025-01-13T16:12:59Z

Examenvragen

← Oudere versie		Versie van 13 jan 2025 18:12
Regel 8:		Regel 8:

	== Examenvragen ==		== Examenvragen ==

			'''Exam of 13/01/2025, Afternoon'''
			No oral question since professor couldn't be present during all exam moments.

			1. You have the structure of a receptor and a few active ligands that inhibit a receptor. There is a structure of the complex. The ligands inhibit the receptor but can not be used as drug. There is a database of drug-like compounds which you need to computationally scan to find active ligands. Which methods could you use and how do they work? Why can't the compounds be optimized further?

			2. 15 multiple choice questions the entire course. There was one question for each of the papers. (15)

			3. The main differences and similarities between genetic algorithms and monte carlo simulated annealing. (10)

			4. Explain the steps of a molecular dynamics simulation. (10)

	'''Exam of 15/01/2024'''		'''Exam of 15/01/2024'''

R0846615 op 17 jan 2024 om 14:44

2024-01-17T14:44:06Z

← Oudere versie		Versie van 17 jan 2024 16:44
Regel 8:		Regel 8:

	== Examenvragen ==		== Examenvragen ==

			'''Exam of 15/01/2024'''

			1. (Oral question) You have the structure of a receptor and a few active ligands that inhibit a receptor. There is no structure of the complex. The ligands inhibit the receptor but can not be used as drug. There is a database of drug-like compounds which you need to computationally scan to find active ligands. Which methods could you use and how do they work? (15)

			2. 15 multiple choice questions about the entire course. There was one question for each of the papers. (15)

			3. The main differences and similarities between genetic algorithms and monte carlo simulated annealing. (10)


	'''Exam of 16/01/2023'''		'''Exam of 16/01/2023'''

R0744698 op 16 jan 2023 om 18:04

2023-01-16T18:04:23Z

← Oudere versie		Versie van 16 jan 2023 20:04
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	3. The main differences and similarities between genetic algorithms and monte carlo simulated annealing. (7)		3. The main differences and similarities between genetic algorithms and monte carlo simulated annealing. (7)

	5. True or false questions (8):		4. True or false questions (8):
	a. The PDB file format the best for proteins and small molecules (drugs) (2)		a. The PDB file format the best for proteins and small molecules (drugs) (2)
	b. A small molecule FF can be used for proteins.(2)		b. A small molecule FF can be used for proteins.(2)

R0744698 op 16 jan 2023 om 18:03

2023-01-16T18:03:45Z

← Oudere versie		Versie van 16 jan 2023 20:03
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	c. The first step in the conjugated gradient method is the same as in the steepest descent. (2)		c. The first step in the conjugated gradient method is the same as in the steepest descent. (2)
	d. The goal of the lead optimization phase is to increase the potency of the molecule. (2)		d. The goal of the lead optimization phase is to increase the potency of the molecule. (2)


	'''Exam of 17/01/2022'''		'''Exam of 17/01/2022'''

R0744698 op 16 jan 2023 om 18:03

2023-01-16T18:03:20Z

← Oudere versie		Versie van 16 jan 2023 20:03
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	[[Categorie: Mabb]]		[[Categorie: Mabb]]
			[[Categorie: Machemie]]

	== Vakinformatie ==		== Vakinformatie ==
	~~Biomolecular modelling~~		Dit vak wordt gegeven door Prof. Arnout Voet. Er zijn enkele dingen veranderd in 2022 vergeleken met de ECTS fiche. Doorheen het semester zijn er enkele verplichte sessies waarbij je de basis leert van werken in UNIX en een molecular dynamics simulation uitvoert, voor aanwezigheid krijg je dan ook punten (ik dacht 1 of 2 op 20, niet zeker). Je moet ook een taak indienen (5/20 punten) waaraan gewerkt wordt tijdens de lessen.

	ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G79AE.htm		ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G79AE.htm

	== Examenvragen ==		== Examenvragen ==

			'''Exam of 16/01/2023'''
			'' (This exam was written instead of oral, due to the Covid-19 restrictions. One open question was replaced by multiple choice questions.)''

			1. 15 multiple choice questions about the entire course. There was one question for each of the papers. (15)

			2. You have the structure of a receptor and a few active ligands that inhibit a receptor. There is no structure of the complex. The ligands inhibit the receptor but can not be used as drug. There is a database of drug-like compounds which you need to computationally scan to find active ligands. Which methods could you use and how do they work? (10)

			3. The main differences and similarities between genetic algorithms and monte carlo simulated annealing. (7)

			5. True or false questions (8):
			a. The PDB file format the best for proteins and small molecules (drugs) (2)
			b. A small molecule FF can be used for proteins.(2)
			c. The first step in the conjugated gradient method is the same as in the steepest descent. (2)
			d. The goal of the lead optimization phase is to increase the potency of the molecule. (2)

	'''Exam of 17/01/2022'''		'''Exam of 17/01/2022'''
	'' (This exam was written instead of oral, due to the Covid-19 restrictions)''		'' (This exam was written instead of oral, due to the Covid-19 restrictions)''

Ninja: /* Examenvragen */

2022-01-17T12:45:27Z

Examenvragen

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 == Examenvragen ==
 '''Exam of 09/01/2021'''
 ''   (This exam was written instead of oral, due to the Covid-19 restrictions)''

Marike: /* Examenvragen */

2021-01-09T12:13:43Z

Examenvragen

@@ Regel 7: / Regel 7: @@
 == Examenvragen ==
 '''Exam of 21/01/2020'''
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 . You have a set of molecules able to bind a target, but they can not be used as drugs. There is a database of drug-like compounds. You have the structure of the active ligands, of the target but not of the complex. What would you do to find new drugs
-. Rndom question: describe the steps of moelcular dynamics
+. Random question: describe the steps of molecular dynamics
 . True or false questions:

Chrt op 23 jan 2020 om 18:26

2020-01-23T18:26:55Z

← Oudere versie		Versie van 23 jan 2020 20:26
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	1. (Oral) Describe Monte Carlo simulation and what it is used for.		1. (Oral) Describe Monte Carlo simulation and what it is used for.

	2. (Oral)Random question: explain the enrichment factor.		2. (Oral)Random question, possible questions are:
			#explain the enrichment factor.
			#describe the set-up of a MD simulation

	3. What is a scoring function and which types are there?		3. What is a scoring function and which types are there?