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Questions related to Bioinformatic Tools
I am running DIYABC for both microsatellite and mtDNA data and testing 3 scenarios. Once I start the analysis I get the following error message: "Something happened during the reftable generation...
09 July 2020 3,830 4 View
Hello, I'm trying to figure out if there's contamination in my DNA samples which affects my sequencing results. Here's the nanodrop data: Sample
02 July 2020 9,064 4 View
I am looking fora command that will modify 3 chains available in the original pdb into a single chain and then renumber all of the residues. I have tried using alter command but when I export the...
27 June 2020 9,253 1 View
On the Zinc15 paper 'ZINC 15−Ligand Discovery for Everyone', 38885 analogs of the Olaparib (40430143) were found as an example of chemical similarity search. I am very far from this result and...
26 June 2020 2,252 0 View
What is the approach used for generic residue numbering of membrane proteins like Serotonin receptors or GPCRs in general? This is particularly challenging when you have a modeled protein that...
25 June 2020 5,220 0 View
Hi everyone, I would like to ask if anyone knows any bioinformatics tool for generating a topological diagram of a protein from its 3D structure?
18 June 2020 2,301 3 View
Columnar formations in basalts are known. These formations are also seen in sandstones but I consider them to be atypical. Few columnar structures of the hexagonal type are known in arensics and...
16 June 2020 6,857 0 View
Hi all, our collaborators would like to perform an RNAseq experiment from a 2-cell co-culture system. For this experiment they would like to co-incubate fibroblasts and macrophages from 2...
15 June 2020 6,757 3 View
Previously, I tried the following link but it doesn't provide search options against PDB database like that of NCBI;...
20 May 2020 2,109 3 View
I'm just learning how to perform an analysis of methylation patterns using bisulfite sequencing data, but I have some questions: 1. What database I can use for obtain bisulfite sequencing...
11 May 2020 1,407 1 View
I'm a molecular biologist, and i have a few projects coming up in transcriptomes and small RNA analysis. Can i get by without knowing any programming using user-friendly software such an Geneious...
11 May 2020 8,003 1 View
Easy to input a linear peptide sequence in the pep-fold server and get the result but how to input the same sequence in N to C terminus cyclization and get the possible cyclic peptide structure?
08 May 2020 9,600 0 View
Greetings 1) For alignment of different sequences of a specific protein together what should be done? Maybe at first we should blast it by uniprot for example, but the sequences of a lot of...
02 May 2020 5,132 4 View
Hi everyone, I need to do MD simulation of wild type and ten variants at 50 ns. I am looking for a low-cost cloud service/ simulation environment. Would you please suggest me any? Thanks in advance.
27 April 2020 3,199 1 View
I have searched on PDB but I didn't succeed in retrieve ACE 2 from PDB. Does there any option to obtain this Enzyme.?
21 April 2020 1,391 1 View
I have 56 genome sequences aligned to one reference genome sequence. Now i want to identify the number of SNPs throughout the genomes, their positions to compare between the 56 query genomes. Is...
20 April 2020 7,326 1 View
I need help regarding In Silico Vaccine Design for Multiple Epitope Construct.
18 April 2020 4,979 0 View
We have a patient-derived antibody that we are characterizing. We know it is binding to SOMETHING in skin cells by our western blot, immunofluorescence, and dissociation assays, but we don't know...
14 April 2020 4,315 0 View
What are the bioinformatic tools that can be used to detect the N and C terminals of protein?
11 April 2020 9,290 2 View
I am reading the following paper. I had a hard time to understand CPMG and CEST and the difference between them. Is there anyone who can explain to me please Structure and Dynamics of an...
10 April 2020 8,490 2 View
Hi, I want to know how efficient are the new metagenomic content prediction tools such as PICRUSt and Piphillin in predicting functions and dynamics ( such as the presence of other genes) using...
07 April 2020 3,848 0 View
I actually have two queries. Biochemical studies suggested presence of an enzyme in an organism but the gene encoding the enzyme is not known. I would like to find out gene candidates based on...
01 April 2020 3,504 2 View
I am developing an algorithm to predict protein complex and I want to measure the GO enrichment for all the predicted complexes which tool should I use to do such analysis for all predicted...
31 March 2020 362 3 View
Hi, I'm a new user of Autodock Vina. I have a problem when validating a docking method for protein-ligand (organic compound). Can anyone explain to me, step by step, how to get a good RMSD...
30 March 2020 1,129 3 View