Brief. Bioinformatics - Evaluating template-based and template-free protein-protein complex structure prediction.

Tópicos

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{ patient(2837) hospit(1953) medic(668) }
{ 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) }
{ sampl(1606) size(1419) use(1276) }
{ gene(2352) biolog(1181) express(1162) }
{ 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) }
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{ structur(1116) can(940) graph(676) }
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{ detect(2391) sensit(1101) algorithm(908) }

Resumo

We compared the performance of template-free (docking) and template-based methods for the prediction of protein-protein complex structures. We found similar performance for a template-based method based on threading (COTH) and another template-based method based on structural alignment (PRISM). The template-based methods showed similar performance to a docking method (ZDOCK) when the latter was allowed one prediction for each complex, but when the same number of predictions was allowed for each method, the docking approach outperformed template-based approaches. We identified strengths and weaknesses in each method. Template-based approaches were better able to handle complexes that involved conformational changes upon binding. Furthermore, the threading-based and docking methods were better than the structural-alignment-based method for enzyme-inhibitor complex prediction. Finally, we show that the near-native (correct) predictions were generally not shared by the various approaches, suggesting that integrating their results could be the superior strategy.

Resumo Limpo

compar perform templatefre dock templatebas method predict proteinprotein complex structur found similar perform templatebas method base thread coth anoth templatebas method base structur align prism templatebas method show similar perform dock method zdock latter allow one predict complex number predict allow method dock approach outperform templatebas approach identifi strength weak method templatebas approach better abl handl complex involv conform chang upon bind furthermor threadingbas dock method better structuralalignmentbas method enzymeinhibitor complex predict final show nearnat correct predict general share various approach suggest integr result superior strategi

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