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12:45, 6 November 2025 Carol talk contribs uploaded File:GraphicSummary PB3.png
12:45, 6 November 2025 Carol talk contribs created page File:Results PSI-BLAST iteration3.png
12:45, 6 November 2025 Carol talk contribs uploaded File:Results PSI-BLAST iteration3.png
11:53, 6 November 2025 Carol talk contribs created page File:GraphicSummary PB2.png
11:53, 6 November 2025 Carol talk contribs uploaded File:GraphicSummary PB2.png
11:19, 6 November 2025 Carol talk contribs created page File:Question2 answer.png
11:19, 6 November 2025 Carol talk contribs uploaded File:Question2 answer.png
10:28, 6 November 2025 Carol talk contribs created page Exercise PSI-BLAST ans (Created page with "NEW answers are being updated! == When BLAST fails == * '''QUESTION 1''': How many significant hits does BLAST find (E-value < 0.005)? Answer: No sequences with E-value below 0.005. ==Trying another approach== * '''QUESTION 2''': How many significant hits does BLAST find (E-value < 0.005)? Answer: After the first iteration, 494 hits are found. * '''QUESTION 3''': How large a fraction of the query sequence do the significant hits match (excluding the identical match)...")
17:49, 5 November 2025 Carol talk contribs created page File:PSI-BLAST firstrun.png
17:49, 5 November 2025 Carol talk contribs uploaded File:PSI-BLAST firstrun.png
14:17, 5 November 2025 Carol talk contribs created page Exercise PSI-BLAST (Created page with "Written by: Carolina Barra Quaglia ==Overview== In this exercise you will learn how to * Critically assess when BLAST fails (e.g., no significant hits) and explore alternative strategies. * Use PSI-BLAST to search for remote homologues of a given protein sequence (an orphan gene). * Interpret iterative PSI-BLAST output (number of hits, coverage, E-value, identity/positives) to assess significance. * Save and reuse a PSSM (profile) to search specialized databases (e.g.,...")
13:49, 5 November 2025 Carol talk contribs created page File:C22orf45.txt
13:49, 5 November 2025 Carol talk contribs uploaded File:C22orf45.txt
16:35, 27 October 2025 Carol talk contribs created page File:Epitopes Malaria exercise.png
16:35, 27 October 2025 Carol talk contribs uploaded File:Epitopes Malaria exercise.png
13:16, 27 October 2025 Carol talk contribs created page File:BepiPred2.png
13:16, 27 October 2025 Carol talk contribs uploaded File:BepiPred2.png
17:32, 9 October 2025 Carol talk contribs created page File:Question7c.png
17:32, 9 October 2025 Carol talk contribs uploaded File:Question7c.png
17:32, 9 October 2025 Carol talk contribs created page File:Question7b.png
17:32, 9 October 2025 Carol talk contribs uploaded File:Question7b.png
17:31, 9 October 2025 Carol talk contribs created page File:Question7a.png
17:31, 9 October 2025 Carol talk contribs uploaded File:Question7a.png
17:31, 9 October 2025 Carol talk contribs created page File:Question4c.png
17:31, 9 October 2025 Carol talk contribs uploaded File:Question4c.png
17:31, 9 October 2025 Carol talk contribs created page File:Question4b.png
17:31, 9 October 2025 Carol talk contribs uploaded File:Question4b.png
17:31, 9 October 2025 Carol talk contribs created page File:Question4a.png
17:31, 9 October 2025 Carol talk contribs uploaded File:Question4a.png
17:30, 9 October 2025 Carol talk contribs created page File:Question3.png
17:30, 9 October 2025 Carol talk contribs uploaded File:Question3.png
17:30, 9 October 2025 Carol talk contribs created page File:Question2.png
17:30, 9 October 2025 Carol talk contribs uploaded File:Question2.png
17:20, 9 October 2025 Carol talk contribs created page Protein Structure answers37 (Created page with "=Protein Structure - Answers= == '''Question 1.''' Look at the method X-RAY diffraction (Å). Which of the complexes is of better quality and why? == The PDB complex 7SBD, has the best resolution (lower Å). == Question 2. Provide a screenshot of the complex == <!-- == Q2 Are all hits are relevant if you are looking for a representative structure of the protein you entered? == No, some of the results (the last four) are not Rhamnogalacturonan acetylesterase at a...")
14:24, 7 October 2025 Carol talk contribs created page File:PyMOL tutorial.pdf
14:24, 7 October 2025 Carol talk contribs uploaded File:PyMOL tutorial.pdf
22:33, 6 October 2025 Carol talk contribs created page File:PyMOL show SEQ.png
22:33, 6 October 2025 Carol talk contribs uploaded File:PyMOL show SEQ.png
22:11, 6 October 2025 Carol talk contribs created page File:PyMOL panels.png
22:11, 6 October 2025 Carol talk contribs uploaded File:PyMOL panels.png
21:53, 6 October 2025 Carol talk contribs created page File:PDB.png
21:53, 6 October 2025 Carol talk contribs uploaded File:PDB.png
21:49, 6 October 2025 Carol talk contribs created page File:Allergen-response.jpg
21:49, 6 October 2025 Carol talk contribs uploaded File:Allergen-response.jpg
19:33, 6 October 2025 Carol talk contribs created page Protein Structure (Created page with "''By Carolina Barra Quaglia'' == Overview == In this exercise you will learn how to * Search diferent protein databases to obtain protein structures. * Critically choose the best structure, when more than one is available. * Visualize a protein structure using PyMOL * Highlight features of interest and perform a basic alignment. This exercise is written a bit different. Instead of the step wise exercise we are going to try a different method called inquiry-based learni...")
16:05, 3 October 2025 User account TA talk contribs was created by WikiSysop talk contribs
15:33, 17 September 2025 Henni talk contribs created page File:Interactive SW example.png
15:33, 17 September 2025 Henni talk contribs uploaded File:Interactive SW example.png
16:20, 27 February 2025 Henni talk contribs created page 22111:Course plan autumn 2025 (Created page with "== General information == === Where and when === Lectures plus subsequent exercises will take place every Tuesday afternoon during the semester, starting '''Tuesday Sep 1 at 13:00'''. Lectures will be from 13:00 to approx. 14 in '''TBA''', and the exercises will then take place in '''TBA'''. === Teachers === * [http://www.dtu.dk/service/telefonbog/person?id=256...")
12:26, 27 November 2024 Henni talk contribs created page File:Ribosomal proteins 34-NJ tree.unrooted.newick.txt

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