search for: qsar

Hello R Users, I am interested in using R to generate quantitative structure-activity relationships (QSARs) for small molecules given a set of molecular descriptors (the X's) and biological data (Y's) (usually tab-delimited data files). Has anyone done this using R ? Would you be willing to share your R scripts (or ideas) for doing this with me ? I am particularly interested in R codes fo...

Dear list: I am interested in the following sort of problem, as is found frequently in the field of QSAR. I have biological activity as a function of chemical structure, with structure defined in a categorical manner in that the SUBSTITUENT is the levels of the POSITION factor. For example, data from Kubinyi (http://www.kubinyi.de/dd-12.pdf) for this type of analysis is presented as follows: factor pa...

Dear all, I am a statistician doing research in QSAR, building regression models where the dependent variable is a numerical expression of some chemical activity and input variables are chemical descriptors, e.g. molecular weight, number of carbon atoms, etc. I am building regression models and I am confronted with a widely a technique called Y-RAND...

...ion we can use our own data distribution to feed on copula as long as we have d, p and q (pdf, cdf and quantile) functions are available. Hence my code for those are: # Make the functions for data distribution dSAR<-function(SAR){dexp(SAR, rate=0.5)} pSAR<-function(SAR){pexp(SAR, rate=0.5)} qSAR<-function(SAR){qexp(c(seq(0,1, .01)),SAR, rate=0.5)} dper<-function(per) {dexp(per,rate=0.5)} pper<-function(per){pexp(per,rate=0.5)} qper<-function(per){qexp(c(seq(0,1,.01)),per, rate=0.5)} gmb<-gumbelCopula(3,dim=2) # create bivariate copula object with dim=2 #tau(gmb) ## const...

Sir, This query is related to randomForest regression using R. I have a dataset called qsar.arff which I use as my training set and then I run the following function - rf=randomForest(x=train,y=trainy,xtest=train,ytest=trainy,ntree=500) where train is a matrix of predictors without the column to be predicted(the target column), trainy is the target column.I feed the same data f...

...gv[5], argv[6]); (debugv(argv) does not produce any output for some reason) Oct 26 02:37:12 qqqqq imap: antispam: calling dspam: /usr/contrib/bin/dspam --source=error --class=spam --signature=490387db858421194018847 --user genie (null) This is the captured output of forked process Oct 26 02:37:12 qsar imap: antispam: dspam returned: ^APdata stack: Out of memory when allocating 1073741840 bytes If I understand correctly, this message is produced by dovecot before it should have launched dspam executable. I don't know why it needs 1GB of stack space for that. Changing dspam to dspamc does no...

Hi: I'm starting a research of Support Vector Regression. I want to obtain a model to predict a property A with a set of property B, C, D, ... This problem is very common for example in QSAR models. I want to know some examples and package that could help me in this way. I know about caret and e1071. But I' don't know if this package can work with continues variables.? Thanks in advance -- View this message in context: http://r.789695.n4.nabble.com/Bigining-with-a-Progr...

Hi all, I would like to do some QSAR analysis (quantitative structure activity relationship). I need to use some Partial Least Squares (PLS) regression, but I have not seen this option on the R-project. Is it possible to do this kind of regression on R? thank you in advance best regards, olivier [[alternate HTML version deleted]]

Error in mvr(Kd_nM ~ qsar, ncomp = 6, data = my, validation = "CV", method = "kernelpls") :   Invalid number of components, ncomp How I can fix this? [[alternative HTML version deleted]]

...t;threehem",header=T) Ym<-as.matrix(hemd[,2]) gvdw.pls<-plsr(Ym ~ Xm,6,method="kernelpls") rsltv<-predict(gvdw.pls,comps=6) plot(Ym,rsltv,type="n",xlab="Actividad + Biol??gica",xlim=c(4.6,6),ylim=c(4.8,6),ylab=" Act. + Biol.(Pred.)",main="QSAR Ligaci??n de Derivados de la Artemisina con + Hemina",sub="Descriptores de Coeficientes VdW") text(Ym,rsltv,labels=threehem$cpd) text(Ym,rsltv,labels=hemd$type,adj=c(0,-1)) --------------------------------------------- threehem: "cpd" "ba" "deox" &quot...

...l worked OK under kernel-3.10.0-1160.76.1.el7.x86_64 and any previous version). The workstations with E5-2609, E5-2650 or E5-2630 are not affected - all of them run qemu-kvm VM under kernel-3.10.0-1160.80.1.el7.x86_64 without problems. Any ideas? Regards, Petko -- Petko Alov Department of QSAR & Molecular Modelling Institute of Biophysics and Biomedical Engineering, BAS 21 G. Bontchev Str 1113 Sofia, BULGARIA

...h an older kernel because of https://bugzilla.redhat.com/show_bug.cgi?id=2143438 , and solved it this way) Regards, Petko On 3/14/23 10:51, Rob Kampen wrote: > Can I edit /etc/default/grub and change > > GRUB_DEFAULT=saved > > to something else? -- Petko Alov Department of QSAR & Molecular Modelling Institute of Biophysics and Biomedical Engineering, BAS 21 G. Bontchev Str 1113 Sofia, BULGARIA phone: +359 2 9793647 mobile: +359 87 7294336 e-mail: petko.alov at biophys.bas.bg

...be used on a per sample basis. These functions are well suited for normalizing chips individually using information from the training set samples. Three vignettes come with the package and include several examples. A few example data sets, mostly from quantitative structure-activity relationship (QSAR) experiments, are also contained in the package. The other two packages, caretLSF and caretNWS, provide alternate versions of caret's train function that can be executed in parallel using the Rlsf and nws packages, respectively. For example, if bootstrapping is used to tune a model, the B mode...

I apologize in advance for posting a question not related to R. I need references to papers that use multiple linear regression in an industrial application and also in a biological experiment. This is aimed to biologists/chemists (non-statisticans) so if anyone has written a brilliant paper where the use of multiple regression is important and also understandable to people with little

...be used on a per sample basis. These functions are well suited for normalizing chips individually using information from the training set samples. Three vignettes come with the package and include several examples. A few example data sets, mostly from quantitative structure-activity relationship (QSAR) experiments, are also contained in the package. The other two packages, caretLSF and caretNWS, provide alternate versions of caret's train function that can be executed in parallel using the Rlsf and nws packages, respectively. For example, if bootstrapping is used to tune a model, the B mode...

Hello, all experts, My major is computer-aied drug design ( main QSAR). Now, my paper need be reviesed, and one reviewer ask me do genetic algorithm coupled with gaussian process method (GA+GP). my data: training set: 191*106 test set: 73*106 here, I need use GA+GP to do variable selection when building the model. In R, there are not GA package like in matla...

This issue has been around for some months, but other things keep crowding out a fix. uname give me 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 yet I have 3.10.0-1160.76.1.el7.x86_64 3.10.0-1160.81.1.el7.x86_64 3.10.0-1160.83.1.el7.x86_64 3.10.0-1160.88.1.el7.x86_64 loaded. The system uses UEFI to boot. sudo ls -l /sys/firmware/efi gives: total 0 -r--r--r--.? 1 root

...iability on the Brain, Alexandru Costan, Radu Tudoran, Benoit Da Mota, Gabriel Antoniu and Bertrand Thirion, INRIA Rennes and Saclay ?02:30 -- 3:00 Very Large Scale Operon Predictions via Comparative Genomics, Ehsan Tabari, ZhengChang Su, UNC Charlotte ?03:00 -- 3:30 Fast Exploration of the QSAR Model Space with e-Science Central and Windows Azure, Jacek Cala, Hugo Hiden, Simon Woodman, Paul Watson, Newcastle University 03:30 - 04:00 Break 04:00 - 05:30 Session 1c Interactive Services ?04:00 -- 4:30 3D Remote Collaboration Framework for Virtual Cultural Heritage, Yasuhide Okamoto,...

...iability on the Brain, Alexandru Costan, Radu Tudoran, Benoit Da Mota, Gabriel Antoniu and Bertrand Thirion, INRIA Rennes and Saclay ?02:30 -- 3:00 Very Large Scale Operon Predictions via Comparative Genomics, Ehsan Tabari, ZhengChang Su, UNC Charlotte ?03:00 -- 3:30 Fast Exploration of the QSAR Model Space with e-Science Central and Windows Azure, Jacek Cala, Hugo Hiden, Simon Woodman, Paul Watson, Newcastle University 03:30 - 04:00 Break 04:00 - 05:30 Session 1c Interactive Services ?04:00 -- 4:30 3D Remote Collaboration Framework for Virtual Cultural Heritage, Yasuhide Okamoto,...

Has this been solved? Is there a bug report I can follow? Thank you for letting me know, Val?re Binet On Wed, Nov 16, 2022 at 2:23 PM Bill Gee <bgee at campercaver.net> wrote: > On the other hand --- I just upgraded one of my CentOS7 systems to > 3.10.0-1160.80.1 today. With that kernel it will not run any KVM guest. > The system hangs - HARD - within one or two seconds of