Hybrid Protein Model (HPM) : A Method For Building A Library Of Overlapping Local Structural Prototypes. Sensitivity Study And Improvements Of The Training: New developments of the Hybrid Protein Model

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(1)Hybrid Protein Model (HPM) : A Method For Building A Library Of Overlapping Local Structural Prototypes. Sensitivity Study And Improvements Of The Training Cristina Benros, Alexandre de Brevern, Serge Hazout. To cite this version: Cristina Benros, Alexandre de Brevern, Serge Hazout. Hybrid Protein Model (HPM) : A Method For Building A Library Of Overlapping Local Structural Prototypes. Sensitivity Study And Improvements Of The Training: New developments of the Hybrid Protein Model. 2003, pp.53-72. �inserm-00133639�. HAL Id: inserm-00133639 https://www.hal.inserm.fr/inserm-00133639 Submitted on 27 Feb 2007. HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés..

(2) HAL author manuscript IEEE International Workshop on Neural Networks for Signal Processing (2003) 53-72. HAL author manuscript.

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(14) HAL author manuscript inserm-00133639, version 1. Ðdæ!à^ç,Ù#ÞfèhéÑà^ÐQÙ,æ ê oRC;EsJMj!IFRPÈWKLTGIO\aPQ|QLe\aPTU¤IFRPÈJoMx&tPdC`S[v{|ZSTxOrRWsPdIFPQWsë-G<P q oRPdJM|dPQ\ÀjTPdJRSTxOPQG&LeJM\ rtS[I;PdJIFEHL[WDrRC;S[IFPQEsJ GFP q oRPQJM|ZP*G^MLTG^jTCFP*L IFWKëÃEsJM|dCFP*LeGFPQ\_ìmJÀI;RP7SeIFRPQC&MLeJM\U¤IFMP JioRxÑPQCS[vtL¶c LeEsWHL[RWKP eê GI;CFo|ÛIFoMCFP*GLeGEKJM|ZC;PQLTG<P*\uRoaII;SlLmWKPQG;G<PQC¤PdYiIFPdJI*_¤VbIIFMP rMCFP*G<PQJTI¤IFEKxOPeUTx`STCFPDIFL[J _ eT rRC;S[I;PdEKJÑG<IFC;oM|ÛI;oRC;PQGL[C;PbL¶c LeEsWHL[RWKPbEsJÑIFRPCFSeIFPdEKJ ê L IL[MLeJRíOî ï _¤kXS ðbPdcePQCQUQIFMEKG\RL[I;L[L[JRíl\aSiPQGJRS[I¤CFPQrRC;PQGFPdJIL[WKWrRCFSeIFPQEsJuvwSTWK\MGDîs *ï LeJM\fIFMP&\aEsñtPQCFPQJTImvwSeWH\RG{LeCFPuJMS[I{P q oL[WKWsëfCFPQrRC;PQGFPdJIFP*\ÈEKJ!I;REKGm\RL IL[MLeJRíÎ_kXPdJ|ZPeU |dSexOrRoaIL I;EsSTJML[WtxOPZIFMSi\MGbLeCFPmEsJI;PdC;PQG<IFPQ\7EsJf\aPZòJREsJMj Tê G<IFC;oM|ZIFoRCL[WtxOSi\RPdWHGvwC;Sex I;RP-G<STWsPÃíiJRS ðWsP*\ajePS[v`GFP q oRPQJM|ZPT_/óÇRPdC;P9LeCFPÃx#L[EKJRWKë IFRC;PdP-|dL[IFPdjTSeC;EsP*G@ôwEáõ ðMPdJÀLfrRCFSeIFPQEsJÃðEI;ÀLÈíiJRS ðJ eê GI;CFoM|ZIFoRC;P#G<L[C;PQGlL jTö÷[SiøXSi\4ùMú G<ûFP ú[q üoMýáþ Pdÿ7JM|døOPÈ÷ EHeÿ\aPdJ ý I;EIë ðEsIFãIFMPhG<IFo\aEsP*\ãGFP q oRPQJM|ZP-îs ï U0ôwEKEHõ ü iû;ÿ; ú ý ðREH| rtPdC;xOEIGlIFS!|MLeC;LT|ÛI;PdC;EsnQP&I;RP#P*GI&|dSexOrML[IFEKREsWKEsIëtPZIðbPdPdJÃI;RPOI;LeCFjTPZI^G<P q oRPdJM|dP LeJM\ÀL Tê rRC;S[I;PdEKJ GI;CFo|ÛIFoMCFP,PdYiIFCLe|ÛI;PQ\ÃvwC;SexßL!JRSTJ C;PQ\RoRJM\RLeJTI`\RL IL[MLeJRíãî ï LeJM\ãòMJMLeWsWKë@ô¯EsEKEáõ LeJM\ x`PdIFRSa\RG7ðREH|´xÈKxOEK|!IFRPrMCFSeIFPdEKJ vwSTWK\REsJRjOoMGFEKJRjOrRiëi ú GF

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(16) HAL author manuscript inserm-00133639, version 1. L ó¤V " EsJRJMPdCXó¤L[íeP*GDV{Ws$W " x`PdIFRSa\MõZ_óÇRPuG<rtPQ|dEòt|ZEsIë,S[vI;RPuk{Dz EHGDIFML[I I;RPEKJavwSeC;x#L I;EsSTJLeG;G<Sa|ZEHL I;PQ\4IFSÀI;RP9\REñÎPdC;PdJI7JRPQoRC;SeJMG#EHG,S cTPdC;WKLerRrREKJRjM_6óÇioMGQU I;RP7xOSa\aEsò|dL[IFEKSeJ SevIFRPfN5\aEHGI;CFEKRoaI;EsSTJMG`LeG;G<Sa|ZEHL I;PQ\ÃI;SIFMP7ðEKJRJREKJRjJRPQoRC;SeJ EKJ 'MoMPdJM|dPQGbIFMPuJRPdoRC;SeJGÇWsSa|dL[IFP*\7EKJhEIGJRPdEKjeitSeC;RSiSa\_ óÇRPuWKEKRC;LeCFë#STaI;LeEsJMPQ\ÈEKGX|dSexOrtSTGFPQ\ÈS[v¤LÑòMJMEI;PuJoMx&tPdCXSev¤G<IFC;oM|ÛI;oRC;LeW|ZWHLeG;G<P*G ô|ZSTCFC;PQGFrSTJM\aEKJRj#I;S,IFMP`JMPdoRC;SeJMGõÛUÎP*Le||dWKLTGFG{EsJM|dWso\aEsJMj7vwCL[jTx`PQJI;GmðEI;9GFEsxOEKWKLeC WKSa|dLeWG<IFC;oM|ÛI;oRCFP*Gd_0óÇRPQGFP&|dWKLTGFGFPQGmL[C;P^CFPQrRC;PQGFPdJI;L[IFEKcePuS[vI;RPOGI;CFoM|ZIFoRCL[WxOS[IFEsv¯G0S[v I;RPurRC;S[I;PdEKJfG<IFC;oM|ÛI;oRC;PQGbvwC;SexI;RP^\RL IL[MLeJRíÎ_ } JÃIFMP,rRC;PQGFPdJI^GI;oM\aëeU¤ðbPOòMC;G<I^rRC;PQGFPdJI^L!G<PQJMGFEI;EsciEsIëL[JMLeWsëaGFEKGlSevDI;RP7kmz I;C;LeEsJMEsJRjÑLe|d|dSeC\aEKJRjlIFS&IFRP0|ZSeJI;CFSTWMrMLeC;Lex`PdIFPQC;GQ_óÇRPQJUiðDPm\aPQG;|ZC;EstPmLeJ#EsxOrRC;S ceP xOPQJTISevI;RPXk{DzIFRC;SeoRjT&I;RPEKJTI;CFSa\ao|ÛIFEKSeJOSevtjL[rMGEKJIFS0IFRP eê rRC;S[I;PdEKJ`G<IFC;oM| I;oRCL[WtvwC;LejexOPdJIGd_z!SeC;PdS cTPdC*UT(L " I;C;LeEsJREKJRjÑEsJh\aPdrRIF) "`GI;C;L[IFPQjeëOPdJMLeRWKPQGDIFS`PZYiIFCLe|ZI I;RPurRC;PZvwPQCFPQJTI;EKLeWtIFCL[JMGFEI;EsSTJMGÇðEsIFREKJfIFRP^kmzÀ_ óÇRPÈk{z CFP*G<oRWsI&EHG^P q oMEsc L[WKPdJIÎ;S*L "TGI;CFoM|ZIFoRCL[WrRCFSeòMWKP "hSeRI;L[EKJRP*\-ë9IFMP xÑoRWsIFEKrRWsPÑWsSa|QL[WL[WKEsjTJRxOPdJI{S[vI;RPÑG<IFC;oM|ZIFoRCL[WÁvwC;LejexOPdJI;GÑôwE¸_ PT_mDN@GFPdC;EKPQGõL[JM\ë \RPZòMJREKJRjÇI;RPDDNbGvwCFP q oMPdJM|dEsP*GL[WKSeJRjbI;RPk{DzÀ_QóÇMPEsJI;CFSa\aoM|ZIFEKSeJuSevjL[rMGPQJML[MWsP*G I;S4EKxOrRCFS cTPI;RPÃG<IFC;oM|ZIFoRC;P9EKJavwSTCFx#L I;EsciEsIë´G<EKxOEsWHL[C;Wsë=I;S=|dSeJicePQJTI;EsSTJML[W0G<P q oRPdJM|dP LeWsEKjeJMx`PQJIOxOPdIFRSa\RGQ_}ÌIÈLeWsWKS ðXGÑòMC;G<IFWKëeUbI;S-I;L[íTPfIFRP!WKPdJRjeIF c L[C;EKLeREKWsEsIë S[v0IFMP C;PdjToRWHL[CG<P*|ZSeJ\RL[C;ëuGI;CFoM|ZIFoRC;PQGÇ+ô RPdWKEsYÑL[JM\ G<MPdPZIÛõEsJIFSlLe|Q|ZSToRJILeJM\ÑGFPQ|dSeJM\RWsëTU I;S#\aPQG;|ZC;EstP0IFRPuMPZIFPQCFSTjePQJRPdEsIë,S[vG<STxOP0WKSa|dLeWGI;CFoM|ZIFoRC;PQGQ_ Ó)¡0à-,mçÈÐZ¡/.6¡7æ!Þ Ó0,mà^ÄÙ,ÞhØ ªl¦ ³¥Q«i®¯° Ë`½¯³¨*Ü£ CFSeIFPQEsJ=NDWKSa|íaGfô¯WKLePQWsP*\ãvwCFSTx N IFSÀDN õ`MLe\ãtPdPdJ \aPdòMJRPQ\=oMGFEKJRjÀL[J oMJMG<oMrPQCFciEHG<P*\#|ZWHLeG;G<EsòMPdCb|ZWKSTGFPÇIFSOgiPdWsv ìmC;ú jTLeJREKndEKJRj^ù zL[r9î ï LeJM\#kXEH\R\aPQJÈzLeCFíTS c zSi\RPdWîs ï UðREH|#I;LeíePQGIFRPmrRCFPdvwPdC;PdJIFEHL[WRIFCL[JMGFEI;EsSTJMGPdYiEHG<IFEKJRj^tPZIðbPdPdJ,IFRP{DNÇG EKJIFS#Le|Q|ZSToRJIQ_óÇRPQGFPuNÇGL[WKWKS ðL`jeSiSa\ÈG<IFC;oM|ÛI;oRCL[WL[rRrMCFS¶YaEKxOL[IFEKSeJÈS[v|ZSexOrRWKPZI;P rMCFSeIFPdEKJ eê G<IFC;oM|ÛI;oRCFP*G{î ï _EKjeoMCFP^0G<MS ðXGIFRP0MLT|ítSeJMPQGSevIFRP` DNÇG{ôwciEHG<o LeWsEKnQL[IFEKSeJhðEsIFhIFM-P 1mz ê GFS[váIðÇL[C;P,î ï õZ_óÇRP^rRC;S[I;PdEKJ!RWsSa|íaGXDN ú IFS7DN L[C;P LTGFGFSa|ZEHL I;PQ\#ðEsIFÈIFR2P GI;C;LeJM\_óÇRPlC;PdjeoMWKLeCD|ZPQJIFCL[3W GI;C;LeJM\#EHGÇCFPQrRCFP*G<PQJIFPQ\,ë I;RPÈDN _óÇRPÈRWKSi|íaG&rRCFEKSeCÑ|ZSeC;C;PQGFrSTJM\9IFSI;RPÈ~ |QL[rMGQU¤IFRP7vwSeWKWsS ðEKJRjhI;SIFMP B |dLerMGQ_Á} JÌFRPmGFLex`PðÇL¶ëuvwSTCIFRPMWsSa|íaGLeG;GFSi|dEKL[IFP*\&ðEsIFÌFM4P RPQWsEsYU[IFMPXRWKSi|í DN ø |dSeC;CFP*G<rtSeJ\RGuI;SIFMPÈC;PdjToRWKLeCÑ|dPdJIFCL[WbrML[CFIÑSev{LC;EKje(I MPdWKEY_ÀóÇRPÈDNÇG vwC;Se6 x 5,IFS LeJM\#I;RSTGFPXvwC;Sex IFS |ML[CLe|ZIFPQCFEKndPXP*GFGFPdJI;EKLeWsWKëÌFRPl~ LeJM\ÈB |dL[rG C;PQGFrtPQ|ÛI;EscTPdWK ëe_¤EsJL[WKWsëTUiIFRP^DNb GbvwC;Seù x I;8S 7,L[C;P0x#LeEsJRWKë#vwSToRJM\fEsJ!|dSeEKWKGQ_ .D³ë§M½Ø¥d¦ µ¤¨[¥*µÁ¦ «Þf§a¥*§a¢¤§M°ÁÜ óÇMPÑ\RL[I;L[L[JRíhoMGFPQ\EsJSToRClGI;oM\aë!EHGm|dSexOrSG<P*\!S[v [#JRSeJ C;PQ\aoRJ\RL[JImrMCFSeIFPdEKJ G<IFC;oM|ZIFoRC;PQGlôwWKPQG;GbIFL[J e S[v¤GFP q oRPQJM|ZPlEH\aPdJI;EIëTU v¯LT|ÛI;SeC _ UiL ûF÷*÷ üDøOÿ9ú UtCFx#G;=\ < VmõDIL[íTPdJÈvwCFSTx/IFMP^ ê N ê NGFEsIFP#î ï _ :;Mú ûF MSeÿ C#eÿPQdLTþQ|ý¯ãú[üý¯rM9÷ CF SeIFPdEKJUDðDP!ML¶cTPfG<IFSTCFP*\ I;RP!G<PQCFEKPQGOSev0\aEKRP*\aC;LeWXL[JRjTWsP*G#L[JM\4IFMP rMCFEKx#L[C;ë=GFP q oRPQJM|ZPT_ p Le|´rRC;S[I;PdEKJMLT|ítSeJMPðbLTG,I;C;LeJMG<vwSeC;x`P*\ EsJI;SãL4GFEKjeJMLeW.

(17) HAL author manuscript inserm-00133639, version 1. >3?A@B CEDGFHJILKMON9PQRDSQTVUEW DXFZY4[\CEQUED]?^R(I&_^QM`N9acb [dIdaèOf&[JIcghUEQ4[JIdi(TCEQjk_ADOTlULUEQXCE?^@WU KR mnTlCEQjoUEQp(UEQ8PQUqUEQjrf. |dSeC;CFP*G<rtSeJ\aEsJMjI;S-IFRPGFoM|d|dPQG;G<EKSeJ=S[v0IFMP\aEsMPQ\aCL[W{LeJRjeWKPQG!tô svu`wOxLuÌõÛ_(óÇRPdJUÇðbP L¶cePÇPdJM|dSa\aPQ\Ì;RPXrRC;S[I;PdEKJ,GI;CFoM|ZIFoRC;PQGS[vÎIFRPm\RL IL[MLeJRí&EKJIFS^GFPdC;EsP*GS[vNÇGQ_ p Le| rMCFSeIFPdEKJG<IFC;oM|ÛI;oRCFP9ðbLTG7GFrRWKEIfEsJIFSãS cePQCFWHL[rRrMEsJRj-vwCL[jTxOPdJI;GQUPQLT|\aPZòMJMPQ\íë LexOEsJRSÃLe|dEK\RG`\aP*GF|dCFEKP*\ ië LeJRjeoMWKLeC&c L[WKoRPQG ¿ ô xy z3{[|U svy z\} ~U xy z\}¶|U svyU xLyÎU svy9&}¶ U xy9d} VU svy9\{¶õÛ_ óÇRP!L[I<IFC;EKRoaIFEKSeJ=S[v0L9rMCFSeIFPdEKJ vwCL[jTxOPdJIÑI;SÀL9DN5EKGOMLTG<P*\ STJ=L9x#L YaEsx#LeW GFEKxÈKWHL[C;EIë4|dCFEsIFPQCFEKSeJÁ_(óÇRP!xOPZI;CFEH|hoMGFPQ\ EHG,L[J p oM|ZWKEK\RPQL[J´\aEHG<I;L[J|ZP|dLeWsWKPQ\ ûF÷*÷ ü ø#î ÿïú _ #:;Mú[ûFÿ eÿdþQý¯ú[üý¯9÷ 9÷ 9ú ;sú û0þ¶9ú ^;Mÿ Ua|dSexOrRoaI;PQ\`vwC;SexIFRPm\aEsMPQ\aCL[WÎL[JRjTWsP*G MSeC¤IFREHGGI;oM\aëTU[PdcTPdC;ë Tê rRC;S[IFPQEsJ`GI;CFo|ÛIFoMCFPDðbLTG¤|doaIEsJIFS0S cePQCFWHL[rMrREsJMj{GI;CFEKJRjG Se~v NÇG^ô 9òRYaPQ\fI;Sf[õÇ|dSeC;CFP*G<rtSeJM\REsJRjÌ;S,WsSa|QL[W Tê G<IFC;oM|ÛI;oRCFP^vwC;LejexOPdJI;GQ_DóÇMP ðMSeWKP^vwCL[jexOPQJTIGl|ZSeJGI;EI;oaIFPÑIFR P "eWsSa|dLeW¤G<IFC;oM|ZIFoRC;P`\ML I;LeML[JM í "M_l}ÌIu|dSeJI;LeEsJG& e GI;CFo|ÛIFoMC;LeWÎvwC;LejexOPdJI;GQ_ ÒÄhÏ¢¤¦ ®¯¬´ªl¦ ³¥Q«i®¯° Ó$³¬¤«i½¯ÒÔ<Ä!ªuÓÖ } J9L[JRSeIFRPQC{rRC;PdciEKSeoMG{rML[rtPdC`î ï UÎðbP^ML¶cePÑ\aPdcTPdWKSertPQ\L#JMS cePdWÁIFCL[EKJREKJRj7L[rMrRCFSLe| |QL[WKWsP*\ "ek{ëiRCFEH\ CFSeIFPdEKJ z!Sa\aPQlW "ãô¯k{DzõÛ_}ÌIGÑjTSTLeWEHG&I;S9|dSexOrMLe|ZI&I;RPÈrMCFSeIFPdEKJ G<IFC;oM|ZIFoRC;PQG&PdJM|dSi\RPQ\ÀEKJIFS9DNÇGÊKJTI;S9|dWsoMG<IFPQC;GÑS[v{|dSeJIFEKjeoMSeoMG eê GI;CFoM|ZIFoRC;P,vwCL[j xOPQJTIGd_OóÇRP#k{Dz EHGu|ZSTxOrSG<P*\Secv G<EsIFP*Gd_ p LT|9GFEI;PÈHGu\aPdòMJRPQ\ÃiëLfWKL¶ðS[v rMCFSTML[REKWKEIë^|dSeC;CFP*G<rtSeJM\REsJRj{IFS0IFMPÇ\REKG<IFC;EsMoaIFEKSeJOS[vIFRPl DNbGQ_kXPdJ|ZPeU[IFRPXkmz |QL[JhtP&C;PdrRC;PQGFPdJIFP*\fëfL#x#L I;CFEsYfSev\aEsxOPQJMG<EKSe=J Y- _bVGI;CFoM|ZIFoRCL[W|ZWHLeG;G^ôwSTC JMPdoRC;SeJõC;PdrRC;PQGFPdJI;GÇL`|ZWKoMG<IFPdCSevÁvwCL[jTx`PQJI;GbðEI;fGFEKxÈKWHL[CWKSi|QL[WG<IFC;oM|ÛI;oRCFPTURL[JM\ÈEHG \RPZòMJRP*\Oirë hGFoM|d|dPQG;G<EKcePÇrRC;SeL[REKWsEsIë&\aEHG<IFC;EsRoRIFEKSeJMSG u<tô y õÛUðEI;/ y \aPdJMS[IFEKJRjuSTJRP SevI;RP! NÇGO ô dÑTU U_s_K_KU õÛ_#óÇðbShGFoM|Q|ZPQG;GFEscTP`G<IFC;oM|ÛI;oRCL[W|ZWHLeG;GFPQGlL[C;POS cePdC WHL[rMrREsJMjOGFEKJM|ZP0IFMPdë7L¶ceP#tô ¶õDGFEsIFPQGXEsJ!|ZSTxOx`STJ_óÇRPlWHLeG<I{G<EsIFPlEHGEsJ!|dSeJIFEKJioREIë.

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(25) PBs. a b c d e f g h i j k l m n o p. 1500 0 500. Numbers. 2500. HAL author manuscript. 9. 13. 18. 23. 28. 33. 38. 43. 48. 53. 58. 63. 68. 73. 78. 83. 88. 93. 98. 103. 109. 115. 1. 5. 9. 13. 18. 23. 28. 33. 38. 43. 48. 53. 58. 63. 68. 73. 78. 83. 88. 93. 98. 103. 109. 115. 1. 5. 9. 13. 18. 23. 28. 33. 38. 43. 48. 53. 58. 63. 68. 73. 78. 83. 88. 93. 98. 103. 109. 115. 1.0. Neq. 0.5. RMSd. 1.5. 2.0. 2 4 6 8 10. 14. 5. 0.0. inserm-00133639, version 1. 1. >3?A@B CED9H4KecLWD8R K_J P CE?Am#[CEQUED?ARÁ(Q9m D]_JPec?âUqCE?^PB UE?^QRQTLUEWDhTlC`K@jD]RUEaXMe JRUqCEQp. +m DCE?^D]m4m ?^DCEaq?UtG?^R m Dn

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