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Questions related to Bioinformatics and Computational Biology
The software should work like this: I choose a molecule; and then the software scans a whole library of many many molecules, and then it quantifies the overlap of each one of them with my target...
08 August 2017 9,064 3 View
factors / parameters for molecular docking result interpretation
08 August 2017 7,900 3 View
Searching for a conference to present my work and get insights in the cutting edge research in my field.
08 August 2017 6,332 2 View
02 August 2017 1,720 2 View
Dear All, I have written a few tcl vmd scripts , those we can also use as VMD commands in tk console. I hope these will be helpful for VMD users. Please have a look at these and let me know your...
07 July 2017 2,278 2 View
Can BLAST perfrom a search including IUPAC ambiguity codes (for example 'M' represents 'A', or 'C'), and 'interpret' their meaning, or are they simply ignored? Thanks!
24 June 2017 9,025 3 View
Iam working with clinical strains isolated from the same hospital and patients with similar background (all CF patients in a CF center). We have the complete sequence of the strains and they are...
22 June 2017 2,242 3 View
The ortholog groups of 5 species proteins look like: Group1: sp1 sp2 sp3 sp4 sp5 Group2: sp1 sp2_seq1 sp2_seq2 sp3 sp4_seq1 sp4_seq2 sp5 (sp is for species here) As here one can see the Group1...
08 June 2017 4,213 1 View
06 June 2017 3,387 3 View
I try to analyse similarity of short protein sequences (30-150 aa) to characterized proteins using NCBI Blast. Typical E-values of my queries range between 0.0001 and 0.97. Following an E-value...
06 June 2017 3,853 4 View
06 June 2017 610 3 View
06 June 2017 6,664 1 View
Dear colleagues, How would you interpret an enrichment factor of 5 that resulted from the evaluation of a molecular docking strategy? Would it mean that within methodology you find 5 times more...
06 June 2017 5,822 3 View
I am trying to calculate SASA scoring function using dock 6.7. However, I am confused about the interpretation of the score. I have obtained: SA_Descriptor Score: 14.15 How could I interpret it?...
05 May 2017 7,521 4 View
I have a peptide sequence whose structure has been solved in 2 different parts by different groups, so I have 2 pdb files. 1st file contains amino-acid sequence 1-42 ( I need only 16-42 from...
05 May 2017 9,276 2 View
Dear colleagues, I have read the Glide user guide (https://isp.ncifcrf.gov/files/isp/uploads/2010/07/gli55_user_manual.pdf) but I am a little bit confused. Is it possible to just calculate the...
05 May 2017 8,246 5 View
Hi everyone! I'm trying to work on the acquisition of the Raman Spectra of a leaf section using Confocal Raman Spectroscopy. The samples to be used are pure, dried, and powdered leaf samples. I am...
18 April 2017 8,722 1 View
04 April 2017 4,638 3 View
Good afternoon, I was wondering if Is there a way to work with a database instead of working with separate files in Autodock? It is computationally expensive to do a process file by file. Since...
04 April 2017 8,628 4 View
I have got a sequence of my human promoter of interest-reporter (pGL4) vector of 3Kbp. The promoter sequence is in capital letters (representing the nucleotides) and the reporter vector sequence...
29 March 2017 4,623 4 View
I need to evaluate the accuracy of predicted interactome of an insect species which I constructed by interolog method. I read that I can use ROCR package for it. I got a gold standard positive PPI...
08 March 2017 6,213 1 View
03 March 2017 3,167 5 View
03 March 2017 9,497 1 View
I need to run codeml for ortholog clusters from different related genus. Do I need to generate a species tree for it that I can use for all the clusters or I need to generate gene tree for all the...
28 February 2017 2,654 3 View