David L. Murphy

10 Questions 20 Answers 0 Followers

Questions related from David L. Murphy

How to experimentally validate/prove a membrane transporter protein transports a specific substrate?

To keep this question short, let's say I have a novel membrane protein with the known structural fold of a known transporter superfamily so I know its function is a transporter of cellular...

18 January 2023 7,577 2 View

Is there a post-genomic database of P.falciparum gene function predictions based on genome loci?

I'm trying to find a bioinformatics/database resource besides something like malariatools, which has gene/protein function predictions based on genome loci context information, however databases...

15 May 2020 6,004 0 View

In what particular environments are Non-photosynthetic cyanobacteria most likely to be found?

Not all cyanobacteria are photosynthetic as several websites claim but maybe most cyanobacteria species probably are photosynthetic Anyway my main question is; In what particular environments...

06 March 2019 10,036 8 View

How is the apicoplast organelle involved in penetration of the host cell (in the parasites invasion) ?

According to a few websites including from wikipedia, The organelle is an adaptation that the apicomplexan applies in penetration of a host cell. Thus how more specifically in cell/molecular...

12 February 2019 1,394 4 View

In apicomplexans like P.falciparum, Why do parasite cell surface proteins appear in the apicoplast organelle?

On plasmodb.org proteins like Stevor and Maurer's cleft which are host-parasite interaction proteins which I presume exist on the parasite cell surface membrane appear with GO annotations for the...

16 January 2019 2,241 4 View

Transmembrane apicoplast proteins are now known to also originate from a vesicle fusion pathway, will any of these still contain signal peptides?

We now know that apicoplast (Trans) membrane proteins can originate from a vesicle and a signal peptide pathway. Normally signal peptide regions are cleaved out of the protein for apicoplast...

15 November 2018 7,596 3 View

In (protein/sturctural bioinformatics), what scenarios is it better to use JackHMMER instead of HHblits?

I have read both the documentation and research articles for HHsuite and HMMER, but in terms of practical usage or tangibility when do individuals in this field prefer to use one of these search...

31 October 2018 7,659 3 View

Are Transmembrane Topology Predictors Reliable Enough For Predicting Transmembrane Proteins?

Transmembrane topology predictors typically predicts alpha helical transmembrane segments within a proteins structure (or the very rare programs which predict transmembrane beta barrel domains)....

17 October 2018 5,804 4 View

Does anyone at the University of Liverpool, or Liverpool School of Tropical Medicine deal with the cellular or molecular biology of P.falciparum?

Hi I'm a Bioinformatics PhD student at UoL. I would like to chat to, or network with anyone who is knowledgeable on the cellular/molecular biology of P.falciparum or related strains/organisms such...

01 January 1970 7,573 6 View

What is the best way to decipher a protein predicted contact map?

Ignoring a proteins sequence, say I have a predicted contact map plotted from a useful tool like ConKit, it can be quite easy to determine general regions of secondary structural features and if...

01 January 1970 6,582 6 View