Hiteshree Buch

15 Questions 11 Answers 0 Followers

Questions related from Hiteshree Buch

How to label the amino acids involved in the protein protein interaction using PyMol software, as shown in expected labels.png?

I want to show the protein-protein interaction as shown in the "expected labels.png" using PyMol software, but unable to do it. Instead, I ended up getting the image shown as "pymol label.png". I...

30 August 2020 1,265 8 View

What should be the problem here in the attached screenshot of python shell from Autodock?

I am performing protein-protein docking using Autodock tools (following https://www.researchgate.net/post/Problem_in_using_Cygwin_commands_for_running_Autodock). I have tried by adding Kollman...

10 August 2020 6,815 4 View

What does this error mean, does the problem reside in protein itself or there is something else to worry about?

I have been trying to convert pdb files of proteins into pdbqt format using Raccoon program from MGLTools-1.5.6. Some of the proteins' files have been successfully converted into pdbqt files but...

24 April 2020 5,246 1 View

I am getting an error while running "make" command in AutoDock4 in ubuntu (virtual box), can anyone have a solution for it?

http://mgldev.scripps.edu/pipermail/autodock/2009-February/005150.html I am following the above link because I also got the error in .dlg file of autodock that MAX_RECORDS of constants.h file has...

16 April 2020 3,147 2 View

How to increase the MAX_RECORDS in constants.h file of autodock 4.0.1 using Windows 10 ?

I am performing protein-protein interaction using AutoDock 1.5.6, but in .dlg file, it throws an error "ERROR: 2328 records read in, but only dimensioned for 2048. Change "MAX_RECORDS" in...

06 April 2020 3,961 6 View

How to iterate a dataframe in a way that each row will be read and test against the svm model and in another file, give predictions of each row?

I am calculating amino acid composition of a fasta file containing 250 protein sequences. the calculated amino acid composition is being saved in a csv file which was read as a dataframe. Bur,...

17 July 2019 2,802 0 View

Why do the best performance of svm tuned model and the prediction accuracy of the same model differ from each other?

I tuned an svm model by giving ranges of gamma and cost's values, from which best performance was obtained as 83.8%. Now, I want to do prediction using the same best model, in order to do so I...

15 April 2019 3,638 0 View

I want to make multiple ROC curves in a single plot using PRROC library. What type of input will go for the same?

I have made a model using tune.svm function of 'e1071' library from R. I tried many times to use 'plot' function of same library but didn't succeeded. Now, if I want to make an ROC plot containing...

02 April 2019 3,859 1 View

Error in UseMethod("predict"): no applicable method for 'predict' applied to an object of class "tune". How to overcome this error?

I have tuned my svm model by setting ranges of 5-5 cost and gamma values using 'e1071' package of r. But the problem comes when I use this model for prediction. The above error has popped up on...

15 March 2019 7,821 3 View

I am doing prediction using r of a file which has 4 classes, but in prediction I am getting one value as x. Why I am getting this extra x?

I am using 'e1071' and 'caret' packages along with SVM algorithm for a file containing 4 classes. In the prediction file, I got a field 'x'. Why this 'x' has come in prediction? I expect the...

08 January 2019 3,416 7 View

Can anyone suggest which software to be used to calculate physico-chemical properties of protein sequences?

I want to calculate physico-chemical properties of protein sequences. can anyone suggest which are the software available out there to do the same.

12 November 2018 3,013 3 View

What is the best way to make dataset for subcellular localization of protein sequences?

I am trying to make dataset in order to predict subcellular localization of protein sequences. I have been downloading sequences from UniProt and ran weka, but accuracy is constantly appearing...

11 October 2018 8,707 1 View

In uniprot i searched for "secreted" location, 5115 sequences were showed, when NOT filter with mitochondrion applied, it gets reduced to 6. Why so?

I want to download sequences which are only present in "secreted subcellular location". So when i searched the same in Uniprot, it was showing 5115 sequences. For more accuracy I applied NOT...

12 September 2018 3,031 0 View

How can I run weka using command line in Windows?

I am trying to run weka, but unfortunately its memory is getting full and showing the error of which screenshot I have attached here. I want to run weka using command "java-Xmx128m-classpath..."...

21 August 2018 9,892 2 View

I am using KUTOOLS to convert a matrix into a single row, which program can I use to convert multiple matrices into single row?

I have a dataset containing 1189 sequences which is in 20*20 matrix, but to use the dataset it must be in straight rows format. I have used KUTOOLS but it only accepts one sequence at a time, so...

19 June 2018 8,857 1 View