My protein of interest has 3D structure available in pdb. I know about an snp that produces short isoform of that protein. How or using what tool I can produce that isoform as a pdb file?
You can use modeller to model the mutant protein by using PDB as template.
You can do it using Swiss PDB viewer, but if you are looking for a tool
this one is great for doing that, just upload your pdb file, write you snp in form of XPosY
and select the chain
http://bleoberis.bioc.cam.ac.uk/duet/stability
it will also calculate all the stability changes upon that mutation
Thanks.
I was trying many tutorials for cnn that I've found online but they are not showing good performance. But my dataset is good enough, when I try with knn or mlp in sklearn I'm getting above 98%...
01 February 2018 3,012 5 View
I was studying about ppi prediction with machine learning approach, then the latest development I've found reported 97% accuracy with DVM hereAccurate prediction of protein-protein interactions by...
11 December 2017 6,716 7 View
I was reading some papers about protein-protein interaction prediction using machine learning. I understood that using various algorithms, all the sequences are transformed into equal length...
09 October 2017 6,877 3 View
I'm looking for a tool that can give how many methyl groups, hydroxyl groups etc. are in a compound from it's SMILES, SDF or MOL2 format.
04 May 2017 9,932 5 View
Is it possible to presume about which Salomonella species present in the sample without using molecular tools like PCR? Just from biochemical tests? If I plan to do PCR for confirming species, how...
09 October 2016 2,202 2 View
I have a list of proteins with their expression metrics. What tools can I use for predicting pathway, cluster analysis etc?
06 July 2016 4,367 2 View
For one of my experiment I need to run a program continuously for a few days. I actually do this in a local cluster. There the head node connects with the slaves with ssh and distribute the work....
04 May 2016 5,779 2 View
I've a receptor and ligand both as pdb file. With mgltools I've converted them to pdbqt. Then performed docking with autodock vina. Now I want my receptor and pdbqt generated by vina to have in a...
01 February 2015 5,001 6 View
I have dataset containing thousands of miRNAs associated with a disease collected from miRTarBase. I need some idea, about what information I can deduce/predict with in-silico/bioinformatic...
01 February 2015 8,780 3 View
I was thinking about applying in some undergraduate summer research programs focused on bioinformatics/computational-biology related field. Google revealed many US institutes but only expects US...
31 December 2014 838 1 View
I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?
11 August 2024 3,115 1 View
I would like to learn more about SPSS and Its application especially in regards to data analysis. Please suggest me how I can learn more about it. Thank you so much.
11 August 2024 9,101 4 View
I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?
11 August 2024 5,138 1 View
Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!
11 August 2024 3,770 4 View
Willett, Shenoy et al. (2021) have developed a brain computer interface (BCI) that used neural signal collected from the hand area of the motor cortex (area M1) of a paralyzed patient. The...
10 August 2024 7,180 0 View
I am developing a predictive model for a water supply network that involves 20 influencing points. However, I only have historical data for 10 out of these 20 points. I would like to know how to...
10 August 2024 4,005 2 View
I'm currently exploring the application of Python in textile engineering, specifically in areas like data analysis, process automation, and the development of smart textiles. I'm interested in...
10 August 2024 7,429 2 View
Usually, additive manufacturing techniques like SEBM, SLS, and SLM are used for interconnected porous lattice structure generation with sizes of >100–200 micrometers. Can the Fused Deposition...
09 August 2024 7,892 0 View
How can I use the cif data obtained from rietveld refinement extracted via gsas2, for microstructural analysis using ETEX software?
09 August 2024 7,718 0 View
I need to model an anisotropic material in which the Poisson's ratio ν_12 ≠ ν_21 and so on. Therefore, the elastic compliance matrix wouldn't be a symmetric one. In ANSYS APDL, for TB,ANEL...
09 August 2024 5,048 2 View