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[(2.)-496.7(Scoring)-332.4(Functions)-332.3(for)-329.1(ProteinProtein)-328.2(Docking)]TJ
/F1 1 Tf
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T*
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T*
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T*
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T*
[(Roset)-8.6(taDock)-299.4(\(Lysko)-7.6(v)-291(and)-294.3(Gray,)-295.6(20)-7.2(08\))-294.5(use)-295.5(physical)-300.9(energy)-294.7(terms)-9.4(.)-290.6(They)-294.9(emp)-7.6(loy)-295.3(a)-292.8(combina)-9.5(tion)-293.1(of)-293.7(Van)-298.2(der)]TJ
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T*
[(Zacharia)-12.1(s,)-286.9(2013\))-290.3(use)-289.8(VdW)-293.3(and)-288.6(elect)-9(rostatic)-294.3(energy)-294.6(calculat)-10.2(ed)-287.8(on)-286.1(a)-287.1(coar)-8.6(se)-289(grained)-292.5(mode)-8.4(ling)-287.4(of)-288(the)-291.4(protein)]TJ
T*
[(to)-254.7(save)-252.5(com)-7.6(putational)-261.2(time.)-259(While)-258.4(it)-251.7(is)-250.2(know)-7(n)-251.2(that)-255.1(prot)-7.8(eins)-253.5(often)-255(change)-260.3(their)-257.8(confo)-7.6(rmations)-259.1(upon)-253.4(binding,)]TJ
T*
[(modeling)-244.6(exib)-7.6(ility)-242.5(is)-238.8(a)-241.6(challe)-9.8(nging)-239.9(problem)-248.7(due)-237.4(to)-243.3(the)-240.2(additi)-9(onal)-240.9(computa)-9.5(tional)-242.3(cost)-242.1(to)-243.3(an)-236.6(already)-248.7(difcul)-8.1(t)]TJ
T*
[(problem)-9.7(.)-233.7(Recent)-245(methods)-242.2(incorpor)-8.9(ate)-236.2(limit)-7(ed)-236.6(exib)-7.6(ility.)-237.2(Exam)-8.2(ples)-236.4(include)-242.1(Swarm)-8.6(Dock,)-242.5(which)-239.9(uses)-240.5(normal)]TJ
/F2 1 Tf
0 67.0005 TD
[(PRED)-9.7(ICTION)-341.7(OF)-334.9(DOC)-8(KED)-338.8(PROT)-9.3(EIN)-336.5(STRU)-9.2(CTURE)-343.7(SIMILAR)-10.7(ITY)-10977.8(893)]TJ
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T*
[(funct)-10.3(ion)-403.4(that)-403(include)-8.7(s)-400.3(a)0(n)-401.7(evol)-7.6(utionary)-408(traces)-408.5(\(ET\))-405(term)-405.8(\(Wilk)-8.2(ins)-404.6(et)-398.7(al.,)-405.2(2012;)-404.9(Mih)-7(alek)-407.7(et)-398.7(al.,)-405.2(2006\),)-404.5(in)]TJ
T*
[(addi)-7.6(tion)-395.5(to)-396.9(the)-399.5(VdW)-395.7(and)-402.4(electrostat)-12.7(ic)-393(com)-7.6(ponent.)-396.5(Th)-7(e)-395.2(assumpt)-10.1(ion)-392(is)-398.1(that)-397.3(binding)-403.5(interfaces)-406.7(tend)-394.6(to)-396.9(be)]TJ
T*
[(evol)-7.6(utionar)-8.9(ily)-332.2(conse)-8.6(rved)-336.9(due)-334.1(to)-334.3(their)-343.2(importanc)-10.1(e.)]TJ
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T*
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[(devised)-257(a)-258.8(backpropagation)-257(n)-.9(eu)4.7(ral)-259.8(n)-.9(et)]TJ
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[(articial)-321.5(n)0(eu)5.6(ron)5.6(s)-1.2(.)-324(T).1(he)-326.2(input)-327.2(layer)-326.4(h)0(o)5.6(l)-2.8(d)5.6(s)-325.6(the)-326.2(i)2.9(np)5.6(ut)-327.2(to)-324.4(the)-326.2(n)5.6(etwo)5.6(rk)-324.4(and)-324.4(s)4.4(ends)-325.6(it)-327.2(to)-324.4(the)-326.2(h)0(idden)-324.4(l)2.9(ay)5.6(er.)-324(E).1(ach)]TJ
T*
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15.3816 0 TD
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21.4932 0 TD
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T*
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T*
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T*
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T*
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T*
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[(89)-7.2(4)-29779.4(AKBAL-)-10.3(DELIBA)-10.7(S)-335.7(E)0(T)-335.3(AL.)]TJ
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[(whe)-8(re)]TJ
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34.5416 0 TD
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7.4718 0 0 6.641 535.8613 532.4597 Tm
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[(is)-335.5(multipl)-8.5(ied)-336.9(with)-336.9(this)-334.1(const)-9.6(ant)-336.9(to)-334.3(avoid)-338.4(bias)-338.8(toward)-339.4(conform)-8.9(ations)-337.4(with)-336.9(small)-10.1(er)-335.3(interface)-12.1(s.)]TJ
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[(Interfac)-10.1(e)-264.3(conser)-10.3(ved)-265.1(atom)-263.8(rati)-9.6(o)-262.5(\(ICAR\))-10.1(:)]TJ
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[(Th)-7(e)-264.3(ratio)-269.2(of)-259.6(the)-268.6(evolu)-8.4(tionarily)-266.4(conse)-8.6(rved)-268.6(interface)-273.9(atoms)-269.2(to)]TJ
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T*
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[(as)-334.6(conse)-8.6(rved.)]TJ
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[(Conservation)-313.6(p)10.7(e)-8.9(r)-316.2(interface)-316.2(a)4.2(tom)-311.5(\()2.3(C)-5.4(P)-1.3(IA)-5.4(\):)]TJ
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[(Av)6.1(er)4.2(age)-308.6(c)-1.3(ons)4.9(e)-1.3(r)4.2(v).4(ation)-312.5(s)5(cor)4.2(e)-308.6(for)-308.8(i)3.4(nter)4.2(fa)4.4(ce)-308.6(atoms.)-312.1(While)]TJ
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[(ICAR)-437.3(fav)5.5(o)-.1(rs)-433.8(co)5.5(nformations)-433.8(with)]TJ
14.4995 0 TD
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[(more)-441.5(interface)-435.8(a)-3.3(toms)]TJ
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[(that)-443.2(ar)-4.2(e)-436.5(c)-4(ons)-3.4(e)1.7(r)-4.2(v)-2.3(ed,)-440(C)-1.3(PIA)-438.7(f)-4.2(avors)-441.6(c)1.7(onfor)-4.2(-)]TJ
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[(mations)-400.8(w)-5.2(ith)-405.3(interface)-407.1(a)-3(toms)-406.5(that)-408(have)-401.4(higher)-401.6(ma)]TJ
21.3452 0 TD
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0 Tc
()Tj
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[(P,)-330.4(V\))-337.5(to)-334.3(the)-336.9(total)-338.2(interf)-10.1(ace)-337.7(size.)]TJ
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[(R\))-332.6(to)-334.3(the)-336.9(total)-338.2(interf)-10.1(ace)-337.7(size.)]TJ
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[(Negativel)-10.5(y)-279.6(charge)-9.1(d)-278.8(ratio:)]TJ
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[(E\))-333.4(to)-334.3(the)-336.9(total)-338.2(interface)-347.8(size.)]TJ
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[(Polar)-258.6(ratio:)]TJ
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