similar to: Cluster analysis of protein time series

I anticipate lacking of prior experience with dimensionality reduction problems. Some scientists concerned with drug discovery performed several steered Molecular Dynamics simulations of the alanine-dipeptide molecule dragged by a radial force from an equilibrium conformation to another different equilibrium conformation. They sampled at regular intervals 7 dihedral angles, 5 bending angles, and

Hi R users This is not related to R but general stats terms. I f any one help me to figure out how they differ and when I need to use which one, i will appreciate it. I read several simulation studies and found that RMSE (Root Mean Square Error) and RMSD (Root Mean Square Difference) appered to be used interchangeablely. The formula for calculating for both RMSE and RMSD are, to me, the

Hi everyone, I have two matrices of 2000x2000 size. They consist of a measurement of RMSD deviations of a protein structure. The basic question i want to answer is the following: are there a significant differences between the two matrices? I aim to use the Mantel test. I don't really know if this is a good idea or if there are better solutions for these mega matrices. Thanks [[alternative

Hi everybody, I'm trying to create a script that picks a txt file with 2 columns of coordinates (depth and variable1) and automatically tries to fit several polynomial with the function nls(). After that, it creates a list of observed, predict, residuals and other, and then it calculates AIC, RMSD, MAD and R^2. At the end of the script I create a series of vectors with MAD for all

Hi , i'm using centos spanish version 4.4, i have installed phpnuke spanish , but i think that apache is showing a strange character ? , when phpnuke (and other php and html pages) shows the ñ or á but in spanish way (? and ?), i would like to know if it is possible changue configuration of apache to show this charactes to the right way Thanks

hello everybody i was seeking a converter beetween R regression output (eg with summary) and the conventional way to present regression output in paper: every model as a vertical vector with \beta, t beetween parenthesis below the first, and other statistics (R^2 etc) . I've seen hmisc and xtable, and if I didn't miss something, they don't include something like that. Thank you

What I am trying to do is use GUI function, traitr, and to call for a pdb file and save it and then display it. I want to call for it by taking it from the user and then displaying it on the screen. I am having problems with that. The line pdb <- read.pdb(""ProteinCode) where proteincode should be the name of the protein, for example 1ly2, but it always ends up being protein. My

Using Trellis, am successfully setting up a number of panels (25) in which I have two box and violin plots. I would like to colour - one plot as RED and the other as BLUE (in each panel). I can do that with the box plots, but the violin density areas just take on one colour. My basic call is as follows: bwplot(rmsd ~ file | code, data=spread_data.filtered, panel = function(...,

Hpa, Dell ships a CD called Dell OpenManage Server Assistant that, starting with version 8.0 released last November, is a Linux-based bootable CD. It uses ISOLINUX to load a linux kernel/initrd combo to start the system. From version 8.0 to 8.2 we use isolinux version 1.66. Starting with version 8.3 we have upgraded to version 2.08. First of all, I'd like to say thanks for your excellent

Dear Colleague, Happy New Year! As we know, codon preference among different species could be dramatically different. To enhance the expression level of a foreign protein in a particular expression system (E.coli, Yeast, Insect, or Mammalian cell), it is very important to adjust the codon frequency of the foreign protein to match that of the host expression system. One classic example is GFP

Dear Colleague, Happy New Year! As we know, codon preference among different species could be dramatically different. To enhance the expression level of a foreign protein in a particular expression system (E.coli, Yeast, Insect, or Mammalian cell), it is very important to adjust the codon frequency of the foreign protein to match that of the host expression system. One classic example is GFP

Dear R users, I would like to align two protein sequences using BLAST (bl2seq). The question is whether this programm have been implemented in R. Thank you for your help, Alla.

When I use vif-route and network-route in the xen-unstable latest release, the script vif-route is executes when I create a new VM , isn''t it? Well the row that begin with ''ip r ...'' that enable routing in Dom0 is not execute by my system when I use ''xm create -c ...''. Are there errors in the script? If I invoke it directly, nothing happens. Excuse me

Hi, After looking without any luck at different places for a working demo for sortable lists I created one. Simple lists are not a problem but lists that looks like a tree seems more complicated. As demo you can have a look at: http://demo.mediafamily.ro/link.php?id=1 What I couldn''t manage is to be able to move the nodes beetween them. For example some childs to move to an upper

Hi! I have some focus problems with wine if I use the managed mode. When I start the application it has focus. But if I switch to another window, and back, then the window gets its focus (the window decorations shows it), but the windows app does not get it. If I click somewhere in the window, then it gets the focus properly, but before that even the shortcuts does not work. With one app it

Dear All, I would like to generate random protein sequences using a HMM model. Has anybody done that before, or would you have any idea which package is likely to be best for that? The important facts are that the HMM will be fitted on ~3 million sequential observations, with 20 different states (one for each amino acid). I guess that 2-5 hidden states should be enough, and an order of 3 would

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

Hi! I have trivial problem with self healing. Maybe somebody will be able to tell mi what am I doing wrong, and why do the files not heal as I expect. Configuration: Servers: two nodes A, B --------- volume posix type storage/posix option directory /ext3/glusterfs13/brick end-volume volume brick type features/posix-locks option mandatory on subvolumes posix end-volume volume server

Hi, I have a PHILIPS CD-RW/DVD-ROM SCB5265 and I have problems reading of some DVDs. I found two different firmware updates which contains .exe files: TD17 (5/1/2007): http://ftp.us.dell.com/rmsd/PHILIPS-SCB5265-TD17.zip TD19 (12/13/2005): http://ftp.us.dell.com/rmsd/SCB5265_fwTD19.zip If I set up the IDE SCSI emulation, the firmware updater can recognize my CD-RW/DVD-ROM drive. # rmmod ide-cd

Il 07/08/20 17:39, Leon Fauster via CentOS ha scritto: > Am 07.08.20 um 17:17 schrieb Alessandro Baggi: >> >> Hi Johnny, >> >> what is the current status of the notification tool for security >> updates on C8? There are possibilities to get soon announces on ML >> for EL8? >> >> Would be great have the tool working. >> >> > >