Validace proteinů:

1.       Najděte v PDBe strukturu cytochromu, získanou pomocí X-ray a mající nejhorší kvalitu.


2.       Obtain information about structure quality for a rhodostomin (PDB ID 4rqg), specifically:

·         How many clashes are there in the structure?

·         Which atom clashes are the closest?

·         How many bond length outliers are in the structure?

·         Which bond length outlier is the highest?

·         How many bond angle outliers are in the structure?

·         Which bond angle outlier is the highest?

Note: Use PDB validation reports for 4rqg.


3.       Protein Data Bank Europe uses summary quality criteria to summarize validation information
about the structure. The summary criteria are: Clashscore, Ramachandran outliers, sidechain
outliers, RSRZ outliers.

Obtain summary criteria for oxy-hemoglobine in methanol (PDB ID 1lfz).



Validace ligandů:

1. Validate all the ligands in the nipah G attachment glycoprotein (PDB ID 3d12). Detect which of
them have missing atoms or wrong chirality and describe where the validation issues are (which
ligand and which atom).

2. Validate a molecule LMG in Plant Photosystem I (PDB ID 2wsc). Detect which atoms are missing.

3.  Validate a molecule of a-carotene (BCR) in Photosystem I (PDB ID 4rku). Detect which atoms
within the ring of this molecule are missing.

4. Detect all estradiol (EST) ligands in Protein Data Bank which have chirality error.

5. Validate biotin (BTN) from 50S Complex (PDB ID 1kqs) and detect which atom is substituted.

6. Validate all sialic acids from PDB and identify the atoms of this molecule at which chirality
errors occur.

7. Validate all samples of these testosterone derivatives: 5-beta-dihydrotestosterone (BDT),
5-alpha-dihydrotestosterone (DHT), epi-testosterone (FFA), testosterone (TES) and testosterone
hemisuccinate (TH2). Detect if there are any samples with chirality errors.