J Chem Inf Model - JGromacs: a Java package for analyzing protein simulations.

Tópicos

{ data(1714) softwar(1251) tool(1186) }
{ model(2220) cell(1177) simul(1124) }
{ sequenc(1873) structur(1644) protein(1328) }
{ structur(1116) can(940) graph(676) }
{ method(1969) cluster(1462) data(1082) }
{ system(1976) rule(880) can(841) }
{ algorithm(1844) comput(1787) effici(935) }
{ system(1050) medic(1026) inform(1018) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ method(1557) propos(1049) approach(1037) }
{ control(1307) perform(991) simul(935) }
{ general(901) number(790) one(736) }
{ perform(999) metric(946) measur(919) }
{ compound(1573) activ(1297) structur(1058) }
{ record(1888) medic(1808) patient(1693) }
{ model(3480) simul(1196) paramet(876) }
{ data(2317) use(1299) case(1017) }
{ can(981) present(881) function(850) }
{ implement(1333) system(1263) develop(1122) }
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{ method(2212) result(1239) propos(1039) }
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{ imag(1947) propos(1133) code(1026) }
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{ measur(2081) correl(1212) valu(896) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ patient(2315) diseas(1263) diabet(1191) }
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{ model(2656) set(1616) predict(1553) }
{ 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) }
{ gene(2352) biolog(1181) express(1162) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ 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) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ 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) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

LABELLED: In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications.AVAILABILITY: JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license .

Resumo Limpo

label paper introduc jgromac java api applic program interfac facilit develop crossplatform data analysi applic molecular dynam md simul api support pars write file format appli gromac groningen machin chemic simul one wide use md simul packag jgromac build strength objectori program java provid multilevel objectori represent simul data integr interconvert sequenc structur dynam inform easytolearn easytous easytoextend framework intend simplifi acceler implement develop complex data analysi algorithm furthermor basic analysi toolkit includ packag programm also provid simpl tool eg xmlbase configur creat applic user interfac resembl commandlin interfac gromac applicationsavail jgromac detail document freeli avail httpsbcbbiochoxacukjgromac gplv licens

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