J Chem Inf Model - Prediction of linear cationic antimicrobial peptides based on characteristics responsible for their interaction with the membranes.


{ model(2656) set(1616) predict(1553) }
{ high(1669) rate(1365) level(1280) }
{ learn(2355) train(1041) set(1003) }
{ can(774) often(719) complex(702) }
{ featur(3375) classif(2383) classifi(1994) }
{ compound(1573) activ(1297) structur(1058) }
{ research(1085) discuss(1038) issu(1018) }
{ spatial(1525) area(1432) region(1030) }
{ can(981) present(881) function(850) }
{ visual(1396) interact(850) tool(830) }
{ take(945) account(800) differ(722) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ clinic(1479) use(1117) guidelin(835) }
{ general(901) number(790) one(736) }
{ gene(2352) biolog(1181) express(1162) }
{ detect(2391) sensit(1101) algorithm(908) }
{ framework(1458) process(801) describ(734) }
{ algorithm(1844) comput(1787) effici(935) }
{ method(1557) propos(1049) approach(1037) }
{ search(2224) databas(1162) retriev(909) }
{ studi(1410) differ(1259) use(1210) }
{ state(1844) use(1261) util(961) }
{ first(2504) two(1366) second(1323) }
{ use(1733) differ(960) four(931) }
{ data(1737) use(1416) pattern(1282) }
{ imag(1057) registr(996) error(939) }
{ method(1219) similar(1157) match(930) }
{ extract(1171) text(1153) clinic(932) }
{ method(984) reconstruct(947) comput(926) }
{ perform(999) metric(946) measur(919) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ research(1218) medic(880) student(794) }
{ use(976) code(926) identifi(902) }
{ drug(1928) target(777) effect(648) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ bind(1733) structur(1185) ligand(1036) }
{ sequenc(1873) structur(1644) protein(1328) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ chang(1828) time(1643) increas(1301) }
{ concept(1167) ontolog(924) domain(897) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ risk(3053) factor(974) diseas(938) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ record(1888) medic(1808) patient(1693) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ patient(2837) hospit(1953) medic(668) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ data(3008) multipl(1320) sourc(1022) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ cancer(2502) breast(956) screen(824) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }


Most available antimicrobial peptides (AMP) prediction methods use common approach for different classes of AMP. Contrary to available approaches, we suggest that a strategy of prediction should be based on the fact that there are several kinds of AMP that vary in mechanisms of action, structure, mode of interaction with membrane, etc. According to our suggestion for each kind of AMP, a particular approach has to be developed in order to get high efficacy. Consequently, in this paper, a particular but the biggest class of AMP, linear cationic antimicrobial peptides (LCAP), has been considered and a newly developed simple method of LCAP prediction described. The aim of this study is the development of a simple method of discrimination of AMP from non-AMP, the efficiency of which will be determined by efficiencies of selected descriptors only and comparison the results of the discrimination procedure with the results obtained by more complicated discriminative methods. As descriptors the physicochemical characteristics responsible for capability of the peptide to interact with an anionic membrane were considered. The following characteristics such as hydrophobicity, amphiphaticity, location of the peptide in relation to membrane, charge density, propensities to disordered structure and aggregation were studied. On the basis of these characteristics, a new simple algorithm of prediction is developed and evaluation of efficacies of the characteristics as descriptors performed. The results show that three descriptors, hydrophobic moment, charge density and location of the peptide along the membranes, can be used as discriminators of LCAPs. For the training set, our method gives the same level of accuracy as more complicated machine learning approaches offered as CAMP database service tools. For the test set accuracy obtained by our method gives even higher value than the one obtained by CAMP prediction tools. The AMP prediction tool based on the considered method is available at http://www.biomedicine.org.ge/dbaasp/.

Resumo Limpo

avail antimicrobi peptid amp predict method use common approach differ class amp contrari avail approach suggest strategi predict base fact sever kind amp vari mechan action structur mode interact membran etc accord suggest kind amp particular approach develop order get high efficaci consequ paper particular biggest class amp linear cation antimicrobi peptid lcap consid newli develop simpl method lcap predict describ aim studi develop simpl method discrimin amp nonamp effici will determin effici select descriptor comparison result discrimin procedur result obtain complic discrimin method descriptor physicochem characterist respons capabl peptid interact anion membran consid follow characterist hydrophob amphiphat locat peptid relat membran charg densiti propens disord structur aggreg studi basi characterist new simpl algorithm predict develop evalu efficaci characterist descriptor perform result show three descriptor hydrophob moment charg densiti locat peptid along membran can use discrimin lcap train set method give level accuraci complic machin learn approach offer camp databas servic tool test set accuraci obtain method give even higher valu one obtain camp predict tool amp predict tool base consid method avail httpwwwbiomedicineorggedbaasp

Resumos Similares

J Chem Inf Model - Classification of compounds with distinct or overlapping multi-target activities and diverse molecular mechanisms using emerging chemical patterns. ( 0,736638916398229 )
J Chem Inf Model - Coping with unbalanced class data sets in oral absorption models. ( 0,700259265233478 )
J Chem Inf Model - Time-split cross-validation as a method for estimating the goodness of prospective prediction. ( 0,699471182971367 )
AMIA Annu Symp Proc - Predicting the dengue incidence in Singapore using univariate time series models. ( 0,696599899623659 )
AMIA Annu Symp Proc - Motivating the additional use of external validity: examining transportability in a model of glioblastoma multiforme. ( 0,69624159674715 )
Artif Intell Med - Training artificial neural networks directly on the concordance index for censored data using genetic algorithms. ( 0,692844023728779 )
J Chem Inf Model - Beyond the scope of Free-Wilson analysis: building interpretable QSAR models with machine learning algorithms. ( 0,689670510319455 )
BMC Med Inform Decis Mak - Concordance and predictive value of two adverse drug event data sets. ( 0,686777559325662 )
AMIA Annu Symp Proc - Effect of data combination on predictive modeling: a study using gene expression data. ( 0,68156026485527 )
J Chem Inf Model - Study of chromatographic retention of natural terpenoids by chemoinformatic tools. ( 0,67527367528152 )
J Chem Inf Model - Comparative studies on some metrics for external validation of QSPR models. ( 0,674268445912937 )
J Chem Inf Model - In silico prediction of aqueous solubility using simple QSPR models: the importance of phenol and phenol-like moieties. ( 0,668812093679183 )
J Chem Inf Model - Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes. ( 0,660545996415183 )
BMC Med Inform Decis Mak - Regression tree construction by bootstrap: model search for DRG-systems applied to Austrian health-data. ( 0,65638113015498 )
J Chem Inf Model - Applicability domain based on ensemble learning in classification and regression analyses. ( 0,656137451460898 )
J Chem Inf Model - iLOGP: a simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. ( 0,646521264764417 )
Comput. Biol. Med. - A prediction model of substrates and non-substrates of breast cancer resistance protein (BCRP) developed by GA-CG-SVM method. ( 0,644697531224667 )
J Chem Inf Model - In silico prediction of chemical Ames mutagenicity. ( 0,643158702670408 )
J Chem Inf Model - Does rational selection of training and test sets improve the outcome of QSAR modeling? ( 0,642238968226974 )
J. Comput. Biol. - The complexity of the dirichlet model for multiple alignment data. ( 0,638464376822867 )
Comput Methods Programs Biomed - A predictive model of longitudinal, patient-specific colonoscopy results. ( 0,637905096304489 )
Int J Health Geogr - Incorporating geographical factors with artificial neural networks to predict reference values of erythrocyte sedimentation rate. ( 0,637574773938128 )
J Chem Inf Model - GRID-based three-dimensional pharmacophores II: PharmBench, a benchmark data set for evaluating pharmacophore elucidation methods. ( 0,634586124344359 )
IEEE Trans Image Process - Incremental N-mode SVD for large-scale multilinear generative models. ( 0,632036500250598 )
J Chem Inf Model - RS-Predictor models augmented with SMARTCyp reactivities: robust metabolic regioselectivity predictions for nine CYP isozymes. ( 0,631256837625143 )
J Chem Inf Model - In silico prediction of total human plasma clearance. ( 0,630715337747816 )
J Chem Inf Model - Binary classification of a large collection of environmental chemicals from estrogen receptor assays by quantitative structure-activity relationship and machine learning methods. ( 0,630345103118156 )
J Chem Inf Model - Development of novel 3D-QSAR combination approach for screening and optimizing B-Raf inhibitors in silico. ( 0,628593441441429 )
J Chem Inf Model - Statistical analysis and compound selection of combinatorial libraries for soluble epoxide hydrolase. ( 0,628366924321489 )
J Chem Inf Model - Oversampling to overcome overfitting: exploring the relationship between data set composition, molecular descriptors, and predictive modeling methods. ( 0,627745204355706 )
J Chem Inf Model - Three useful dimensions for domain applicability in QSAR models using random forest. ( 0,626735703746555 )
J Chem Inf Model - Rank order entropy: why one metric is not enough. ( 0,625877040158013 )
J Chem Inf Model - Optimizing predictive performance of CASE Ultra expert system models using the applicability domains of individual toxicity alerts. ( 0,621263144893669 )
J Biomed Inform - Markov blanket-based approach for learning multi-dimensional Bayesian network classifiers: an application to predict the European Quality of Life-5 Dimensions (EQ-5D) from the 39-item Parkinson's Disease Questionnaire (PDQ-39). ( 0,616013909258292 )
J Chem Inf Model - Ligand and structure-based classification models for prediction of P-glycoprotein inhibitors. ( 0,615731483099491 )
BMC Med Inform Decis Mak - Measuring preferences for analgesic treatment for cancer pain: how do African-Americans and Whites perform on choice-based conjoint (CBC) analysis experiments? ( 0,614249745548376 )
J Chem Inf Model - Pharmacophore assessment through 3-D QSAR: evaluation of the predictive ability on new derivatives by the application on a series of antitubercular agents. ( 0,612771155760918 )
J Chem Inf Model - Analysis and study of molecule data sets using snowflake diagrams of weighted maximum common subgraph trees. ( 0,61196863359716 )
J Chem Inf Model - Real external predictivity of QSAR models. Part 2. New intercomparable thresholds for different validation criteria and the need for scatter plot inspection. ( 0,605018805310607 )
AMIA Annu Symp Proc - Advanced proficiency EHR training: effect on physicians' EHR efficiency, EHR satisfaction and job satisfaction. ( 0,602865428504771 )
Int J Health Geogr - Comparative analysis of remotely-sensed data products via ecological niche modeling of avian influenza case occurrences in Middle Eastern poultry. ( 0,601937977368759 )
IEEE Trans Image Process - Neighborhood Supported Model Level Fuzzy Aggregation for Moving Object Segmentation. ( 0,599133116403396 )
J Chem Inf Model - In silico prediction of chemical acute oral toxicity using multi-classification methods. ( 0,597863878152505 )
J Chem Inf Model - Hsp90 inhibitors, part 1: definition of 3-D QSAutogrid/R models as a tool for virtual screening. ( 0,594642859101723 )
Geospat Health - Indirect field technology for detecting areas object of illegal spills harmful to human health: application of drones, photogrammetry and hydrological models. ( 0,594617924687575 )
Comput Methods Programs Biomed - Kinetic modelling of haemodialysis removal of myoglobin in rhabdomyolysis patients. ( 0,594174501745957 )
J. Med. Internet Res. - A case study of the New York City 2012-2013 influenza season with daily geocoded Twitter data from temporal and spatiotemporal perspectives. ( 0,594122290777169 )
J Am Med Inform Assoc - Harvest: an open platform for developing web-based biomedical data discovery and reporting applications. ( 0,593152081299927 )
J Chem Inf Model - A new approach to radial basis function approximation and its application to QSAR. ( 0,586070235036207 )
Med Biol Eng Comput - Application of the RIMARC algorithm to a large data set of action potentials and clinical parameters for risk prediction of atrial fibrillation. ( 0,585750337315752 )
Artif Intell Med - Fuzzy model identification of dengue epidemic in Colombia based on multiresolution analysis. ( 0,585732427843531 )
J Chem Inf Model - Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection. ( 0,584899584513915 )
J Biomed Inform - MysiRNA: improving siRNA efficacy prediction using a machine-learning model combining multi-tools and whole stacking energy (G). ( 0,579816450200879 )
Spat Spatiotemporal Epidemiol - Spatial approximations of network-based individual level infectious disease models. ( 0,579461963047181 )
Spat Spatiotemporal Epidemiol - Spatial modelling of disease using data- and knowledge-driven approaches. ( 0,579193213630673 )
J Chem Inf Model - A multiscale simulation system for the prediction of drug-induced cardiotoxicity. ( 0,578159327034472 )
IEEE Trans Image Process - Gait-based person recognition using arbitrary view transformation model. ( 0,576885346514417 )
Comput. Aided Surg. - Evaluation of a computational model to predict elbow range of motion. ( 0,576672992410066 )
J Chem Inf Model - GA(M)E-QSAR: a novel, fully automatic genetic-algorithm-(meta)-ensembles approach for binary classification in ligand-based drug design. ( 0,574512072628214 )
J Chem Inf Model - Applicability Domain ANalysis (ADAN): a robust method for assessing the reliability of drug property predictions. ( 0,573782364003928 )
Methods Inf Med - Supporting regenerative medicine by integrative dimensionality reduction. ( 0,572678699187235 )
Comput Math Methods Med - Multiscale autoregressive identification of neuroelectrophysiological systems. ( 0,570677900684978 )
J Integr Bioinform - Using variable precision rough set for selection and classification of biological knowledge integrated in DNA gene expression. ( 0,568135605473577 )
J Chem Inf Model - Design and synthesis of new antioxidants predicted by the model developed on a set of pulvinic acid derivatives. ( 0,563957515735703 )
Brief. Bioinformatics - Identifying driver mutations from sequencing data of heterogeneous tumors in the era of personalized genome sequencing. ( 0,563778499689529 )
J Chem Inf Model - Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets. ( 0,562505831415512 )
J Chem Inf Model - How experimental errors influence drug metabolism and pharmacokinetic QSAR/QSPR models. ( 0,562193423432333 )
IEEE Trans Image Process - The segmentation of the left ventricle of the heart from ultrasound data using deep learning architectures and derivative-based search methods. ( 0,561405426989964 )
J Biomed Inform - Selection of interdependent genes via dynamic relevance analysis for cancer diagnosis. ( 0,560216748378074 )
Methods Inf Med - Investigating recurrent neural networks for OCT A-scan based tissue analysis. ( 0,556293487982489 )
J Chem Inf Model - A comparison of different QSAR approaches to modeling CYP450 1A2 inhibition. ( 0,555814287891484 )
Comput. Biol. Med. - Quantification of contributions of molecular fragments for eye irritation of organic chemicals using QSAR study. ( 0,555236768045107 )
J Chem Inf Model - Automated building of organometallic complexes from 3D fragments. ( 0,553989142021793 )
Comput. Biol. Med. - Extracting predictive SNPs in Crohn's disease using a vacillating genetic algorithm and a neural classifier in case-control association studies. ( 0,553293771698473 )
Int J Med Inform - Design and implementation of I2Vote--an interactive image-based voting system using windows mobile devices. ( 0,553239321447234 )
J Biomed Inform - Improving record linkage performance in the presence of missing linkage data. ( 0,552377646992621 )
J Am Med Inform Assoc - Choosing blindly but wisely: differentially private solicitation of DNA datasets for disease marker discovery. ( 0,552089274408628 )
J Chem Inf Model - Predictions of BuChE inhibitors using support vector machine and naive Bayesian classification techniques in drug discovery. ( 0,551331883683447 )
J Chem Inf Model - Experimental and computational prediction of glass transition temperature of drugs. ( 0,550279327644194 )
J Chem Inf Model - Four-dimensional structure-activity relationship model to predict HIV-1 integrase strand transfer inhibition using LQTA-QSAR methodology. ( 0,549902348829396 )
Brief. Bioinformatics - An empirical assessment of validation practices for molecular classifiers. ( 0,549280312009066 )
J Chem Inf Model - Best of both worlds: combining pharma data and state of the art modeling technology to improve in Silico pKa prediction. ( 0,54921941763887 )
Int J Comput Assist Radiol Surg - Assessing performance in brain tumor resection using a novel virtual reality simulator. ( 0,549164841280785 )
IEEE Trans Neural Netw Learn Syst - ML-Tree: a tree-structure-based approach to multilabel learning. ( 0,548533254135322 )
J Chem Inf Model - Impact of template choice on homology model efficiency in virtual screening. ( 0,548495291595114 )
Med Biol Eng Comput - Optimal design of clinical tests for the identification of physiological models of type 1 diabetes in the presence of model mismatch. ( 0,548303063270605 )
J Chem Inf Model - CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. ( 0,54715876676645 )
Med Biol Eng Comput - Validating motor unit firing patterns extracted by EMG signal decomposition. ( 0,54517434184043 )
J Chem Inf Model - Jointly handling potency and toxicity of antimicrobial peptidomimetics by simple rules from desirability theory and chemoinformatics. ( 0,544715253270684 )
Neural Comput - Input statistics and Hebbian cross-talk effects. ( 0,544580830837993 )
Comput Methods Programs Biomed - An attribute weight assignment and particle swarm optimization algorithm for medical database classifications. ( 0,542768839995609 )
Artif Intell Med - A machine learning-based approach to prognostic analysis of thoracic transplantations. ( 0,540795305993616 )
J Chem Inf Model - Estimation of carcinogenicity using molecular fragments tree. ( 0,537624484546189 )
J Biomed Inform - Transfer learning based clinical concept extraction on data from multiple sources. ( 0,537218054622326 )
J Chem Inf Model - Pre-processing feature selection for improved C&RT models for oral absorption. ( 0,535073365520256 )
J Chem Inf Model - Combined 3D-QSAR, molecular docking, and molecular dynamics study on piperazinyl-glutamate-pyridines/pyrimidines as potent P2Y12 antagonists for inhibition of platelet aggregation. ( 0,53492063145223 )
Comput. Biol. Med. - In silico prediction of spleen tyrosine kinase inhibitors using machine learning approaches and an optimized molecular descriptor subset generated by recursive feature elimination method. ( 0,534640861247496 )
J Med Syst - A new data preparation method based on clustering algorithms for diagnosis systems of heart and diabetes diseases. ( 0,533695701727833 )
Comput Methods Programs Biomed - Modeling the glucose regulatory system in extreme preterm infants. ( 0,530963057975681 )
J Am Med Inform Assoc - Use of a support vector machine for categorizing free-text notes: assessment of accuracy across two institutions. ( 0,529836347239584 )