J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions.

Tópicos

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

Resumo

The identification of modules in protein structures has major relevance in structural biology, with consequences in protein stability and functional classification, adding new perspectives in drug design. In this work, we present the comparison between a topological (spectral clustering) and a geometrical (k-means) approach to module identification, in the frame of a multiscale analysis of the protein architecture principles. The global consistency of an adjacency matrix based technique (spectral clustering) and a method based on full rank geometrical information (k-means) give a proof-of-concept of the relevance of protein contact networks in structure determination. The peculiar "small-world" character of protein contact graphs is established as well, pointing to average shortest path as a mesoscopic crucial variable to maximize the efficiency of within-molecule signal transmission. The specific nature of protein architecture indicates topological approach as the most proper one to highlight protein functional domains, and two new representations linking sequence and topological role of aminoacids are demonstrated to be of use for protein structural analysis. Here we present a case study regarding azurin, a small copper protein implied in the Pseudomonas aeruginosa respiratory chain. Its pocket molecular shape and its electron transfer function have challenged the method, highlighting its potentiality to catch jointly the structure and function features of protein structures through their decomposition into modules.

Resumo Limpo

identif modul protein structur major relev structur biolog consequ protein stabil function classif ad new perspect drug design work present comparison topolog spectral cluster geometr kmean approach modul identif frame multiscal analysi protein architectur principl global consist adjac matrix base techniqu spectral cluster method base full rank geometr inform kmean give proofofconcept relev protein contact network structur determin peculiar smallworld charact protein contact graph establish well point averag shortest path mesoscop crucial variabl maxim effici withinmolecul signal transmiss specif natur protein architectur indic topolog approach proper one highlight protein function domain two new represent link sequenc topolog role aminoacid demonstr use protein structur analysi present case studi regard azurin small copper protein impli pseudomona aeruginosa respiratori chain pocket molecular shape electron transfer function challeng method highlight potenti catch joint structur function featur protein structur decomposit modul

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