02881nas a2200325   4500008004100000022001400041245011500055210006900170260011100239300001200350490000700362520173200369653001702101653001902118653001902137653002002156653003402176653001602210653001502226653002102241653001802262653001602280100001502296700001802311700001502329700002302344700003302367700002602400856012902426       2015                        eng d  a1386-207300aStudy of applications of machine learning based classification methods for virtual screening of lead molecules0 aStudy of applications of machine learning based classification m  aEXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATESbBENTHAM SCIENCE PUBL LTDcAUG  a658-6720 v183 a<p>The ligand-based virtual screening of combinatorial libraries employs a number of statistical modeling and machine learning methods. A comprehensive analysis of the application of these methods for the diversity oriented virtual screening of biological targets/drug classes is presented here. A number of classification models have been built using three types of inputs namely structure based descriptors, molecular fingerprints and therapeutic category for performing virtual screening. The activity and affinity descriptors of a set of inhibitors of four target classes DHFR, COX, LOX and NMDA have been utilized to train a total of six classifiers viz. Artificial Neural Network (ANN), k nearest neighbor (k-NN), Support Vector Machine (SVM), Naive Bayes (NB), Decision Tree - (DT) and Random Forest - (RF). Among these classifiers, the ANN was found as the best classifier with an AUC of 0.9 irrespective of the target. New molecular fingerprints based on pharmacophore, toxicophore and chemophore (PTC), were used to build the ANN models for each dataset. A good accuracy of 87.27% was obtained using 296 chemophoric binary fingerprints for the COX-LOX inhibitors compared to pharmacophoric (67.82 %) and toxicophoric (70.64 %). The methodology was validated on the classical Ames mutagenecity dataset of 4337 molecules. To evaluate it further, selectivity and promiscuity of molecules from five drug classes viz. anti-anginal, anti-convulsant, anti-depressant, anti-arrhythmic and anti-diabetic were studied. The TPC fingerprints computed for each category were able to capture the drug-class specific features using the k-NN classifier. These models can be useful for selecting optimal molecules for drug design.</p>10aAnti-anginal10aanti-arrythmic10aanti-bacterial10aanti-convulsant10aanti-depressant anti-diabetic10abinary QSAR10achemophore10amachine learning10apharmacophore10atoxicophore1 aVyas, Renu1 aBapat, Sanket1 aJain, Esha1 aTambe, Sanjeev, S.1 aKarthikeyan, Muthukumarasamy1 aKulkarni, Bhaskar, D.  uhttps://library.ncl.res.in/content/study-applications-machine-learning-based-classification-methods-virtual-screening-lead-002122nas a2200193   4500008004100000245016100041210006900202260000800271300001000279490000700289520137600296100001501672700001801687700001501705700003301720700001901753700002601772856013001798       2016                        eng d00aBuilding and analysis of protein-protein interactions related to diabetes mellitus using support vector machine, biomedical text mining and network analysis0 aBuilding and analysis of proteinprotein interactions related to   cDEC  a37-440 v653 aIn order to understand the molecular mechanism underlying any disease, knowledge about the interacting proteins in the disease pathway is essential. The number of revealed protein-protein interactions (PPI) is still very limited compared to the available protein sequences of different organisms. Experiment based high-throughput technologies though provide some data about these interactions, those are often fairly noisy. Computational techniques for predicting protein protein interactions therefore assume significance. 1296 binary fingerprints that encode a combination of structural and geometric properties were developed using the crystallographic data of 15,000 protein complexes in the pdb server. In a case study, these fingerprints were created for proteins implicated in the Type 2 diabetes mellitus disease. The fingerprints were input into a SVM based model for discriminating disease proteins from non disease proteins yielding a classification accuracy of 78.2% (AUC value of 0.78) on an external data set composed of proteins retrieved via text mining of diabetes related literature. A PPI network was constructed and analysed to explore new disease targets. The integrated approach exemplified here has a potential for identifying disease related proteins, functional annotation and other proteomics studies. (C) 2016 Elsevier Ltd. All rights reserved.1 aVyas, Renu1 aBapat, Sanket1 aJain, Esha1 aKarthikeyan, Muthukumarasamy1 aTambe, Sanjeev1 aKulkarni, Bhaskar, D.  uhttps://library.ncl.res.in/content/building-and-analysis-protein-protein-interactions-related-diabetes-mellitus-using-support