Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ method(2212) result(1239) propos(1039) }
{ monitor(1329) mobil(1314) devic(1160) }
{ first(2504) two(1366) second(1323) }
{ process(1125) use(805) approach(778) }
{ method(1219) similar(1157) match(930) }
{ problem(2511) optim(1539) algorithm(950) }
{ perform(999) metric(946) measur(919) }
{ cost(1906) reduc(1198) effect(832) }
{ method(984) reconstruct(947) comput(926) }
{ group(2977) signific(1463) compar(1072) }
{ high(1669) rate(1365) level(1280) }
{ imag(1947) propos(1133) code(1026) }
{ studi(2440) review(1878) systemat(933) }
{ concept(1167) ontolog(924) domain(897) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ model(2220) cell(1177) simul(1124) }
{ search(2224) databas(1162) retriev(909) }
{ risk(3053) factor(974) diseas(938) }
{ data(1737) use(1416) pattern(1282) }
{ error(1145) method(1030) estim(1020) }
{ algorithm(1844) comput(1787) effici(935) }
{ design(1359) user(1324) use(1319) }
{ care(1570) inform(1187) nurs(1089) }
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{ data(3963) clinic(1234) research(1004) }
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{ compound(1573) activ(1297) structur(1058) }
{ data(3008) multipl(1320) sourc(1022) }
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{ activ(1138) subject(705) human(624) }
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{ extract(1171) text(1153) clinic(932) }
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{ patient(2837) hospit(1953) medic(668) }
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{ data(2317) use(1299) case(1017) }
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{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ sampl(1606) size(1419) use(1276) }
{ gene(2352) biolog(1181) express(1162) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ can(981) present(881) function(850) }
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{ structur(1116) can(940) graph(676) }
{ cancer(2502) breast(956) screen(824) }
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{ drug(1928) target(777) effect(648) }
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{ survey(1388) particip(1329) question(1065) }
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{ activ(1452) weight(1219) physic(1104) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

The structural comparison of proteins is a vital step in structural biology that is used to predict and analyse a new unknown protein function. Although a number of different techniques have been explored, the study to develop new alternative methods is still an active research area. The present paper introduces a text modelling-based technique for the structural comparison of proteins. The method models the secondary and tertiary structure of proteins in two linear sequences and then applies them to the comparison of two structures. The technique used for pairwise comparison of the sequences has been adopted from computational linguistics and its well-known techniques for analysing and quantifying textual sequences. To this end, an n-gram modelling technique is used to capture regularities between sequences, and then, the cross-entropy concept is employed to measure their similarities. Several experiments are conducted to evaluate the performance of the method and compare it with other commonly used programs. The assessments for information retrieval evaluation demonstrate that the technique has a high running speed, which is similar to other linear encoding methods, such as 3D-BLAST, SARST, and TS-AMIR, whereas its accuracy is comparable to CE and TM-align, which are high accuracy comparison tools. Accordingly, the results demonstrate that the algorithm has high efficiency compared with other state-of-the-art methods.

Resumo Limpo

structur comparison protein vital step structur biolog use predict analys new unknown protein function although number differ techniqu explor studi develop new altern method still activ research area present paper introduc text modellingbas techniqu structur comparison protein method model secondari tertiari structur protein two linear sequenc appli comparison two structur techniqu use pairwis comparison sequenc adopt comput linguist wellknown techniqu analys quantifi textual sequenc end ngram model techniqu use captur regular sequenc crossentropi concept employ measur similar sever experi conduct evalu perform method compar common use program assess inform retriev evalu demonstr techniqu high run speed similar linear encod method dblast sarst tsamir wherea accuraci compar ce tmalign high accuraci comparison tool accord result demonstr algorithm high effici compar stateoftheart method

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