Lon W. R. Fong

10 Questions 8 Answers 0 Followers

Questions related from Lon W. R. Fong

How to handle big data sets (>10GB) in R Bioconductor packages?

I am running an R script that downloads and preprocesses all the available methylation data sets from TCGA. I'm using the Bioconductor package MethylMix for this. However, when I try to process...

04 September 2018 10,088 4 View

How can I identify which genes in a list are most functionally similar to a given gene?

I have a gene, let's say p300, and I have a list of genes that are co-expressed with it. I want to find which of these genes have the most similar function to p300. What would be the best tool for...

23 July 2018 5,760 3 View

Script or program to select top-scoring poses from an SDF file?

I have an SDF of docking results generated in smina (spin-off of AutoDock VINA with the ability to handle SDFs). Each compound has five poses that were generated, but I need to get rid of all but...

30 June 2018 2,276 2 View

Is it necessary to normalize gene expression data when comparing survival between patients with and high and low expression of a gene based on median?

I'm doing some preliminary analysis on a list of genes of interest, and I was using a data set that contains RNA-seq data from patients and the corresponding clinical information, including...

22 May 2018 8,093 4 View

What is your method for analyzing results from AutoDock VINA?

Specifically, for a virtual screen of 50,000~200,000 compounds, how many binding modes (poses) per compound do you usually ask VINA to generate? And how do you analyze these results? Visually...

20 April 2018 7,630 5 View

How to choose concentration range of drug for cancer-cell proliferation assay?

I'm a student in computational drug design, but I'm going to move to the bench soon to test some compounds we've designed. I've been reading the methods sections of some papers describing novel...

29 March 2018 5,716 5 View

Should I perform energy minimization on a homology-modeled holo form of an enzyme for molecular docking?

I'm homology-modeling the ubiquitin-bound form of a deubiquitinase for which only the apo form is available as a crystal structure, using a homolog that has a crystal structure with ubiquitin...

28 November 2017 8,814 4 View

Can blind docking be used to determine which ligands are most likely to bind a known binding site?

I know that blind docking is most often used to determine an unknown binding site, but can it be used to determine whether a ligand is thermodynamically more likely to bind a given (known) binding...

10 October 2017 9,946 6 View

Is it okay to passage suspension cells by simply adding more media to the culture flask?

I have some HL60 and U937 cells I'm growing in 50mL of media in T75 flasks, and I was wondering if it would be okay to do a 1:2 split by just adding 50mL more media to the same flask instead of...

14 March 2017 4,019 3 View

How do I Subset a Matrix in R by Selecting Rows Whose Values for a Column Equal Those in a Vector?

Hello all, I have a matrix of gene-expression data from 50 samples whose rows are the probes and whose columns are the samples. There is an additional column consisting of the Entrez gene IDs for...

29 September 2015 6,381 8 View