For all questions illustrate your answers fully, describing what you did at every step and providing input/output illustrating what input/output was obtained. You need to include, embedded, within your submitted work all relevant output from online servers, as appropriate, as well as a written dialogue to fully illustrate what work you carried out. For all parts describe how you obtained your data by stating the bioinformatics portal used and the search strategy. Please quote accession numbers of all database files used.
(a)Locate within the Protein Data Bank (PDB) the 3-D structure of a complex between HIV-1 protease and an inhibitor molecule. State what your chosen entry is,and download the coordinates for the structure to use with a molecular graphics program to investigate your chosen structure.
This question I was using this program call protein data bank (PDB) I was searching HIV-1 protease and an inhibitor then I found this codes 1HIH Show screenshot of your search, after I press the code 1HIH it takes me to the homepage of the 3D view structure then I take screenshots take copy and past to the Microsoft words.
(b)Using one of the programs rasmol, Jmol or Swiss-PDB Viewer produce an image of the protein that you think clearly illustrates the major structural features within the enzyme and highlights the binding site of the inhibitor molecule. State the commands used within the selected program to obtain your image.
In PDB I downloaded the 3D coordinates file in molecular graphics programs such as Swiss-PDB viewer the file I download from the top right-hand side of the page and download as a PDB format the I save this code in my laptop after I use swiss-PDB view program to see the image. You have just loaded the PDB file into Swiss-PDB viewer. Now you should produce a nice image showing the structural features of the enzyme and showing the inhibitor binding.
(c)Using tools within the PDB investigate the interactions between the inhibitor and its receptor site. Illustrate with images the different types of interactions that exist and give details of these interactions in your discussion.
I was accessing the and entry 1HIH codes. This structure contains in addition to the protein molecule of Hiv-1 and Hiv-2 proteases in the complex. I scroll down the file to small molecules section, and I click on the ligand interaction tab this ligand I take screenshots to take copy and past to Microsoft word. Much more needed here. You have screenshot of H-bonds but no discussion of where those bonds are between the protein and inhibitor. Also what about the other interactions? Click on each in turn, show the screenshot and then discuss what you see i.e. which atoms the bonds are between.
(d)Discuss which types of bioinformatics tools and programs could be used to design new potentially improved inhibitors for HIV-1 protease.
PDBSUM is a database – yes it’s a database NOT a program to design new inhibitors located at the European Bioinformatics Institue (EBI) if you go to this website www.ebi.ac.uk/pdbsum and find PDB code 1HIH, summary this information are given about the protein. The Uniprot file for this protein is cross-reference (P0ABH0) along with Pfam derived domain information as well as PubMed information. Drug or inhibitor molecules of the intermolecular interactions can be easily visualized using this tool. Discuss here programs that will design new inhibitors.
These two table shows different funtional partners.different protein interaction to and known interation are from cerate database also experimetally determined.
(a)Use the UniProt to obtain the files for the two human forms of GAP3DH. Carry out an alignment of the protein sequences using NALIGN from the EBI portal. Comment on the similarities and differences in the primary structure of the two forms.
I start using this Uniprot database of this website www.uniprot.org to search GAP3DH I have open this two files P04406 and 014556 I scroll through the files to find the information about the sequence and find the fast file format of the sequence, and then I copy the sequence I open this program EBI Kalign I run both the sequence in one file then I got the result of, The Clustal multiple sequence alignment by Kalign is showing seven lanes of sequence, and the first line shows some sequence is missing, the other line is identical.this screenshot shows three amino acid are identical and the length is 335.
(b)For both forms of GAP3DH use the STRING portal to identify possible protein partners. In each case use the Settings menu to display two shells of interactions, with 10 interacting partners in each shell. Summarise your findings.
From 014556 this GAP3DH is lineage all the protein and roted around nodes.
from P04406 this GAP3DH is lineage all the protein and roted around nodes.
(c)Using the information obtained in parts (a) and (b) comment on the functional differences between the two forms of GAP3DH.
Glyceraldehyde-3-phospate dehydrogenase (GAPDH) is associated with essential cell catabolic procedures and, as it is believed to be persistently communicated, has a place with the gathering of housekeeping qualities. In this way, it is as often as possible utilized as an interior control in quantitative quality articulation examines. Notwithstanding, the proof of various articulation designs in an expansive scope of life forms and tissues, just as the event of various isoforms, demonstrates that GAPDH must be reconsidered as an interior control in qPCR studies, and its comment must be advanced. GAPDH has been demonstrated to be engaged with the pathway of vitality and carbon atom supply just as in interpretation and apoptosis. In the current investigation, we detached the two isoforms, GAPDH-1 and GAPDH-2, of the gilthead ocean bream (Sparus aurata) and the European ocean bass (Dicentrarchus labrax).
Discuss what you did to run the homology modelling with screenshots- this is where most of the marks are awarded.
SWISS-PROT is a huge database that describes the protein sequences and provides information of the functions of the proteins, post-transcriptional modifications, domain structure of the protein. The global quality estimation or the QMEAN of the structure was -6.68 with a GMQE of 0.45 and the sequence identity between them is 20.86% . The second structure of the template was estimated using SWISS-PROT. The structural similarity predicted by the database was 19.13%. The QMEAN and GMQE values were -6.53 and 0.53 respectively. In this way, the structural similarity of the target protein with different templates was matched.
Much more discussion needed here. DISCUSS, in detail, the results of the modelling that you obtain, including an in-depth discussion of ALL of the models obtained, the template used by the program for each model, and all of the key features of the models produced and their quality as shown from the output generated.
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