J Chem Inf Model - Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method.

Tópicos

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

Resumo

We focused on the parametrization and evaluation of empirical models for fast and accurate calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartree-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models reproduced quantum mechanics level charges well and were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.

Resumo Limpo

focus parametr evalu empir model fast accur calcul conform depend atom charg protein model base electroneg equal method eem parametr procedur tailor protein use larg protein fragment refer structur fit eem model paramet use atom charg comput three popul analys mulliken natur iter hirshfeld hartreefock level two basi set g g two environ gas phase implicit solvat parametr success valid eem model test insulin ubiquitin model reproduc quantum mechan level charg well consist respect popul analysi basi set specif model show averag correl rmsd e averag absolut error per atom e eem model can use freeli avail eem implement eemsolv

Resumos Similares

Brief. Bioinformatics - Critical assessment of high-throughput standalone methods for secondary structure prediction. ( 0,6722279143657 )
J Biomed Inform - Protein contact map prediction using multi-stage hybrid intelligence inference systems. ( 0,623988252131251 )
Comput Biol Chem - Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues. ( 0,597024522675554 )
Comput Math Methods Med - Prediction of BP reactivity to talking using hybrid soft computing approaches. ( 0,595084515045051 )
Med Decis Making - Identifying individual changes in performance with composite quality indicators while accounting for regression to the mean. ( 0,584306547468143 )
J Clin Monit Comput - Comprehensive diagnosis of whole-body acid-base and fluid-electrolyte disorders using a mathematical model and whole-body base excess. ( 0,582296493213366 )
Comput Methods Programs Biomed - Single stage and multistage classification models for the prediction of liver fibrosis degree in patients with chronic hepatitis C infection. ( 0,565098650320311 )
Comput Math Methods Med - Validation in principal components analysis applied to EEG data. ( 0,559599971897408 )
J Chem Inf Model - Drug-like density: a method of quantifying the bindability of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank. ( 0,5525 )
Comput Math Methods Med - Transcriptional protein-protein cooperativity in POU/HMG/DNA complexes revealed by normal mode analysis. ( 0,551156238003305 )
Comput Math Methods Med - Epitope mapping of metuximab on CD147 using phage display and molecular docking. ( 0,546211595847266 )
Comput Biol Chem - Improved homology model of cyclohexanone monooxygenase from Acinetobacter calcoaceticus based on multiple templates. ( 0,541384977788225 )
Med Biol Eng Comput - Quantitative evaluation of upper-limb motor control in robot-aided rehabilitation. ( 0,540881864633454 )
J Med Syst - Effective automated prediction of vertebral column pathologies based on logistic model tree with SMOTE preprocessing. ( 0,540696359167418 )
J Chem Inf Model - Acetylcholinesterase inhibitors: structure based design, synthesis, pharmacophore modeling, and virtual screening. ( 0,537533376943193 )
Int J Health Geogr - Urban slum structure: integrating socioeconomic and land cover data to model slum evolution in Salvador, Brazil. ( 0,525251462945701 )
Brief. Bioinformatics - Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. ( 0,520620162865693 )
Brief. Bioinformatics - Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. ( 0,520378732422101 )
Int J Health Geogr - Application of satellite precipitation data to analyse and model arbovirus activity in the tropics. ( 0,51871942760921 )
Comput. Biol. Med. - Prediction of protein functions based on function-function correlation relations. ( 0,518072562118507 )
Artif Intell Med - Quantitative prediction of MHC-II binding affinity using particle swarm optimization. ( 0,516134074549813 )
J Biomed Inform - Prediction of influenza vaccination outcome by neural networks and logistic regression. ( 0,512569285782198 )
Methods Inf Med - Sensor-based fall risk assessment--an expert 'to go'. ( 0,512315961610742 )
Int J Comput Assist Radiol Surg - New method for internal anal sphincter measurements: feasibility study. ( 0,511570101374398 )
J Chem Inf Model - Homology modeling of human muscarinic acetylcholine receptors. ( 0,511158080184974 )
Med Biol Eng Comput - Is principal component analysis an effective tool to predict face attractiveness? A contribution based on real 3D faces of highly selected attractive women, scanned with stereophotogrammetry. ( 0,510430759187859 )
Appl Clin Inform - Comparing predictions made by a prediction model, clinical score, and physicians: pediatric asthma exacerbations in the emergency department. ( 0,510016860340187 )
J Chem Inf Model - Antiviral atropisomers: conformational energy surfaces by NMR for host-directed myxovirus blockers. ( 0,509789973722211 )
BMC Med Inform Decis Mak - Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis. ( 0,509542261772523 )
J. Comput. Biol. - Prediction of siRNA potency using sparse logistic regression. ( 0,509517868032303 )
J Chem Inf Model - Structural protein-ligand interaction fingerprints (SPLIF) for structure-based virtual screening: method and benchmark study. ( 0,5076819231709 )
Brief. Bioinformatics - Ranking prognosis markers in cancer genomic studies. ( 0,506718654723748 )
Comput Biol Chem - Colonic amyloidosis, computational analysis of the major amyloidogenic species, Serum Amyloid A. ( 0,506276225787761 )
Comput Biol Chem - An ensemble method for prediction of conformational B-cell epitopes from antigen sequences. ( 0,505304535472242 )
Comput Math Methods Med - Advances and computational tools towards predictable design in biological engineering. ( 0,503713557104832 )
Int J Health Geogr - Identifying malaria vector breeding habitats with remote sensing data and terrain-based landscape indices in Zambia. ( 0,503053737748824 )
Int J Health Geogr - Modeling larval malaria vector habitat locations using landscape features and cumulative precipitation measures. ( 0,501782536848099 )
Int J Health Geogr - Small-scale health-related indicator acquisition using secondary data spatial interpolation. ( 0,501352962411884 )
Comput. Biol. Med. - LRRsearch: An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors. ( 0,500512136501629 )
J Biomed Inform - Sparse modeling of spatial environmental variables associated with asthma. ( 0,500164446641513 )
Comput Biol Chem - Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. ( 0,499756038043539 )
Artif Intell Med - Machine learning for improved pathological staging of prostate cancer: a performance comparison on a range of classifiers. ( 0,497723386979189 )
Int J Med Robot - Anatomical comparison and evaluation of human proximal femurs modeling via different devices and FEM analysis. ( 0,496662331493227 )
AMIA Annu Symp Proc - Early prediction of the response of breast tumors to neoadjuvant chemotherapy using quantitative MRI and machine learning. ( 0,495860524315526 )
Spat Spatiotemporal Epidemiol - Multivariate Bayesian spatial model of preterm birth and cardiovascular disease among Georgia women: Evidence for life course social determinants of health. ( 0,494812650795201 )
Comput Biol Chem - PPM-Dom: a novel method for domain position prediction. ( 0,494316465685875 )
Med Biol Eng Comput - A dynamic Bayesian network for estimating the risk of falls from real gait data. ( 0,494148662279784 )
Comput Methods Programs Biomed - Adaptive network based on fuzzy inference system for equilibrated urea concentration prediction. ( 0,494112784584931 )
Neural Comput - Sample skewness as a statistical measurement of neuronal tuning sharpness. ( 0,492694184332184 )
IEEE J Biomed Health Inform - Identification of microsatellites in DNA using adaptive S-transform. ( 0,492221372143298 )
IEEE J Biomed Health Inform - Design and evaluation of RFID deployments in a trauma resuscitation bay. ( 0,491210625687066 )
J. Comput. Biol. - Enhancing Gibbs sampling method for motif finding in DNA with initial graph representation of sequences. ( 0,491056241910124 )
Med Decis Making - Standard error of measurement of 5 health utility indexes across the range of health for use in estimating reliability and responsiveness. ( 0,490939309812997 )
J Am Med Inform Assoc - An improved model for predicting postoperative nausea and vomiting in ambulatory surgery patients using physician-modifiable risk factors. ( 0,490289247704531 )
Int J Health Geogr - An objective index of walkability for research and planning in the Sydney metropolitan region of New South Wales, Australia: an ecological study. ( 0,489636629526589 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,489237727410273 )
Comput Methods Programs Biomed - Circular Cone: a novel approach for protein ligand shape matching using modified PCA. ( 0,489221367906676 )
J Chem Inf Model - HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors. ( 0,488477934784248 )
Comput. Biol. Med. - A knowledge-driven probabilistic framework for the prediction of protein-protein interaction networks. ( 0,488386767445008 )
Int J Med Robot - Intraoperative measurement of femoral antetorsion using the anterior cortical angle method: a novel use for smartphones. ( 0,486890939222787 )
Int J Health Geogr - Modelling typhoid risk in Dhaka metropolitan area of Bangladesh: the role of socio-economic and environmental factors. ( 0,485348682052728 )
Int J Comput Assist Radiol Surg - A computer analysis method for correlating knee X-rays with continuous indicators. ( 0,48493074586257 )
J Med Syst - A new approach: role of data mining in prediction of survival of burn patients. ( 0,48473169679813 )
J Chem Inf Model - Cavities tell more than sequences: exploring functional relationships of proteases via binding pockets. ( 0,483675939214442 )
Comput. Biol. Med. - Remote homology detection incorporating the context of physicochemical properties. ( 0,482635193622658 )
J. Comput. Biol. - A probabilistic model for sequence alignment with context-sensitive indels. ( 0,481768247915053 )
Int J Health Geogr - Comparing the accuracy of two secondary food environment data sources in the UK across socio-economic and urban/rural divides. ( 0,481658502251022 )
J Chem Inf Model - The ensemble performance index: an improved measure for assessing ensemble pose prediction performance. ( 0,480670319495552 )
J Chem Inf Model - FRED pose prediction and virtual screening accuracy. ( 0,480142979436078 )
Comput Biol Chem - Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: the role of mixing statistics and frame shift of neighboring genes. ( 0,479445292459461 )
J Chem Inf Model - PocketAlign a novel algorithm for aligning binding sites in protein structures. ( 0,479062389115275 )
J Chem Inf Model - Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA. ( 0,479030906169065 )
BMC Med Inform Decis Mak - Artificial neural network models for prediction of cardiovascular autonomic dysfunction in general Chinese population. ( 0,478683707963125 )
Comput Methods Programs Biomed - Exploring an optimal vector autoregressive model for multi-channel pulmonary sound data. ( 0,478463476077096 )
J Chem Inf Model - Prediction of the dissociation constant pKa of organic acids from local molecular parameters of their electronic ground state. ( 0,478087495419986 )
J. Comput. Biol. - Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. ( 0,477996875155296 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,477645417694255 )
Comput. Biol. Med. - A joint sparse representation-based method for double-trial evoked potentials estimation. ( 0,477474530955153 )
Comput. Biol. Med. - Signal peptide discrimination and cleavage site identification using SVM and NN. ( 0,476438427509642 )
AMIA Annu Symp Proc - When you can't tell when it hurts: a preliminary algorithm to assess pain in patients who can't communicate. ( 0,476029879638584 )
Comput Biol Chem - Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions. ( 0,474872547183665 )
Med Decis Making - Performance of a mathematical model to forecast lives saved from HIV treatment expansion in resource-limited settings. ( 0,47437871130988 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,47389006425849 )
J Chem Inf Model - Different binding modes of structurally diverse ligands for human D3DAR. ( 0,473737776534689 )
Brief. Bioinformatics - Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations. ( 0,473637494573458 )
Comput Biol Chem - Systematic analysis of an amidase domain CHAP in 12 Staphylococcus aureus genomes and 44 staphylococcal phage genomes. ( 0,472321166668146 )
Med Decis Making - Performance profiling in primary care: does the choice of statistical model matter? ( 0,472014310402865 )
J Chem Inf Model - TFD: Torsion Fingerprints as a new measure to compare small molecule conformations. ( 0,469666341781844 )
Comput Methods Programs Biomed - Prediction of postprandial blood glucose under uncertainty and intra-patient variability in type 1 diabetes: a comparative study of three interval models. ( 0,469171558408555 )
J Chem Inf Model - Prediction of ligand-induced structural polymorphism of receptor interaction sites using machine learning. ( 0,469171558408555 )
J Chem Inf Model - An integrated computational analysis of the structure, dynamics, and ligand binding interactions of the human galectin network. ( 0,468695819031363 )
J Chem Inf Model - Capturing the crystal: prediction of enthalpy of sublimation, crystal lattice energy, and melting points of organic compounds. ( 0,467763686642468 )
Comput. Biol. Med. - Pre-operative prediction of surgical morbidity in children: comparison of five statistical models. ( 0,466625854243401 )
Comput Math Methods Med - A voxel-map quantitative analysis approach for atherosclerotic noncalcified plaques of the coronary artery tree. ( 0,466252404120157 )
Curr Protoc Bioinformatics - An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design. ( 0,465418010019631 )
J Clin Monit Comput - Cardiac index measurements by transcutaneous Doppler ultrasound and transthoracic echocardiography in adult and pediatric emergency patients. ( 0,465376953792564 )
Neural Comput - Quantifying statistical interdependence, part III: N > 2 point processes. ( 0,465184586230567 )
J Chem Inf Model - TRAPP: a tool for analysis of transient binding pockets in proteins. ( 0,464834840100684 )
Comput Math Methods Med - Statistical evaluation of a fully automated mammographic breast density algorithm. ( 0,464719995172409 )
J Med Syst - Quantitative grading using Grey Relational Analysis on ultrasonographic images of a fatty liver. ( 0,464602553573358 )