PoseBusters：基于 AI 对接方法的局限性分析

瀵艰

PoseBusters 鎻ず浜嗗熀浜?AI 鐨勫垎瀛愬鎺ユ柟娉曞湪鐢熸垚鐗╃悊涓婂彲琛岀殑鏋勮薄鍜屾硾鍖栬兘鍔涙柟闈㈢殑灞€闄愩€?/p>

• 馃И 鍩轰簬 AI 鐨勫垎瀛愬鎺ユ柟娉曠殑閫熷害涓庡噯纭€?/li>
• 馃攳 鐗╃悊鍙鎬у拰娉涘寲鑳藉姏鐨勮瘎浼?/li>
• 馃洜 PoseBusters 宸ュ叿鍖呯殑搴旂敤鍙婅瘎浼?/li>

杩戝勾鏉ワ紝鍩轰簬娣卞害瀛︿範鐨勮泲鐧借川-閰嶄綋瀵规帴鎶€鏈繀閫熷彂灞曪紝鍏堕€熷害鍜屽噯纭€у睍鐜板嚭宸ㄥぇ娼滃姏銆備絾娣卞叆鍒嗘瀽鍙戠幇锛屽敖绠¤繖浜涙妧鏈湪鏅朵綋缁撴瀯鐨勬牴鍧囨柟鍋忓樊锛圧MSD锛変笂琛ㄧ幇浼樺紓锛屼絾瀹冧滑甯稿父鐢熸垚鐗╃悊涓婁笉鍚堢悊鐨勫垎瀛愮粨鏋勩€傚洜姝わ紝浠呯敤 RMSD 鏉ヨ瘎浼拌繖浜涙妧鏈槸涓嶅厖鍒嗙殑锛屽挨鍏舵槸鍦ㄨ瘎浼板熀浜庢繁搴﹀涔犵殑鏂规硶鏃讹紝杩橀渶鑰冭檻绌洪棿鍜岃兘閲忔爣鍑嗐€?/p>

PoseBusters 鏄竴涓娇鐢ㄦ垚鐔熺殑鍖栧淇℃伅瀛﹀伐鍏峰寘 RDKit 杩涜鏍囧噯璐ㄩ噺妫€鏌ョ殑 Python 鍖呫€侾oseBusters 閫氳繃楠岃瘉閰嶄綋鐨勫寲瀛﹀拰鍑犱綍涓€鑷存€э紝濡傜珛浣撳寲瀛︺€佽姵棣欑幆鐨勫钩闈㈡€с€佹爣鍑嗛敭闀垮強铔嬬櫧璐?閰嶄綋鐨勭鎾烇紝鏉ユ楠屽叾鐗╃悊鍙鎬с€傚彧鏈夐偅浜涢€氳繃杩欎簺妫€鏌ワ紝骞堕娴嬪嚭鎺ヨ繎澶╃劧鐨勭粨鍚堟ā寮忕殑鏂规硶锛屾墠鑳借璁や负鏄€屽ソ鐨勬瀯璞°€嶇殑銆?/p>

閫氳繃 PoseBusters锛屼綔鑰呮瘮杈冧簡浜旂鍩轰簬娣卞害瀛︿範鐨勫鎺ユ柟娉曪紙DeepDock銆丏iffDock銆丒quiBind銆乀ankBind 鍜?Uni-Mol锛夊拰涓ょ鎴愮啛鐨勬爣鍑嗗鎺ユ柟娉曪紙AutoDock Vina 鍜?CCDC Gold锛夛紝鍖呮嫭鏄惁閲囩敤鍒嗗瓙鍔涘鍔涘満鐨勯澶栧悗澶勭悊棰勬祴鑳介噺鏈€灏忓寲姝ラ銆?/p>

鐮旂┒鍙戠幇锛屽湪鐗╃悊鍙鎬у拰娉涘寲鑳藉姏鏂归潰锛屾病鏈変换浣曚竴绉嶅熀浜庢繁搴﹀涔犵殑鏂规硶鑳借秴瓒婁紶缁熷鎺ュ伐鍏枫€傛澶栵紝鍒嗗瓙鍔涘鍔涘満琛ュ厖浜嗘繁搴﹀涔犳柟娉曟墍缂哄け鐨勫鎺ョ浉鍏崇墿鐞嗙煡璇嗐€?/p>

鍩轰簬 DL 鐨勫鎺ユ柟娉?/h2>

鐮旂┒璋冩煡浜嗕簲绉嶄笉鍚岀殑鍩轰簬 DL 鐨勫鎺ユ柟娉曪細

1. DeepDock锛氬熀浜庨厤浣撳師瀛愯窛绂诲拰缁撳悎鍙ｈ琛ㄩ潰缃戞牸鐨勭粺璁℃綔鑳姐€?/li>
2. DiffDock锛氬湪鐩插鎺ヤ腑浣跨敤绛夊彉鍥剧缁忕綉缁滅殑鎵╂暎杩囩▼銆?/li>
3. EquiBind锛氫篃鏄湪鐩插鎺ヤ腑浣跨敤绛夊彉鍥剧缁忕綉缁溿€?/li>
4. TankBind锛氫竴绉嶇敤浜庨娴嬬粨鍚堝彛琚嬩腑瀵规帴鐨勫熀浜庝笁瑙掓祴閲忕殑绁炵粡缃戠粶鏂规硶銆?/li>
5. Uni-Mol锛氶泦鎴愬彛琚嬬瓑鍙樺彉鎹㈠櫒杩涜瀵规帴銆?/li>

杩欎簺鏂规硶鍚勮嚜鎻愪緵浜嗕竴绉嶇嫭鐗圭殑鏋勮薄棰勬祴鏂瑰紡锛屽嚫鏄句簡鍩轰簬 DL 鎶€鏈殑澶氭牱鎬с€傚畠浠湪 PDBbind 閫氱敤闆嗙殑瀛愰泦涓婅繘琛屼簡璁粌锛孌eepDock 浣跨敤鐨勬槸 v2019 鐗堟湰锛屽叾浠栨柟娉曚娇鐢ㄧ殑鏄?v2020 鐗堟湰銆?/p>

缁忓吀瀵规帴鏂规硶

浣滀负瀵规瘮锛岀爺绌惰繕鍖呮嫭浜嗕袱绉嶆垚鐔熺殑闈?DL 鏂规硶锛欰utoDock Vina 鍜?Gold銆傝繖浜涙柟娉曚负璇勪及鍩轰簬 DL 鐨勬柟娉曞湪棰勬祴鍖栧鍜岀墿鐞嗕笂鏈夋晥鐨勬瀯璞℃柟闈㈢殑鎬ц兘鎻愪緵浜嗗熀鍑嗐€?/p>

姣忕鏂规硶浣跨敤鐨勫崗璁拰杞欢鐗堟湰鍦ㄧ爺绌剁殑琛ュ厖鏉愭枡涓湁璇︾粏璇存槑銆傚€煎緱娉ㄦ剰鐨勬槸锛屼笉鍚屾柟娉曚箣闂寸殑鎼滅储绌洪棿瀹氫箟鍚勪笉鐩稿悓锛屾湁浜涢渶瑕佸畾涔夌殑缁撳悎浣嶇偣锛岃€屾湁浜涘湪鏁翠釜铔嬬櫧涓婅繘琛岀洸鎼滅储銆?/p>

PoseBusters 娴嬭瘯濂椾欢

PoseBusters 濂椾欢鍦ㄦ湰鐮旂┒涓嚦鍏抽噸瑕侊紝鍒嗕负涓夌被锛?/p>

1. 鍖栧鏈夋晥鎬у拰涓€鑷存€?/strong>锛氬寘鎷鍖栧缁撴瀯琛ㄧず鐨勬鏌ヤ互鍙婇娴嬪拰鐪熷疄閰嶄綋涔嬮棿鐨勪竴鑷存€ф鏌ャ€?/li>
2. 鍒嗗瓙鍐呮湁鏁堟€?/strong>锛氫晶閲嶄簬鐗╃悊鍙俊搴︾殑娴嬭瘯锛屽寘鎷敭闀裤€佽搴﹀拰鍐呴儴璺濈锛屼互鍙婄敤浜庢瀯璞″彲淇″害鐨勮兘閲忚绠椼€?/li>
3. 鍒嗗瓙闂存湁鏁堟€?/strong>锛氳瘎浼拌泲鐧借川-閰嶄綋鍜岄厤浣?杈呭洜瀛愪箣闂寸殑鐩镐簰浣滅敤锛屽寘鎷窛绂诲拰浣撶Н閲嶅彔娴嬭瘯銆?/li>

璇勪及鏍囧噯

璇勪及鏍囧噯鍖呮嫭棰勬祴閰嶄綋鍜屾櫠浣撻厤浣撲箣闂存渶灏忛噸鍘熷瓙鏍瑰潎鏂瑰亸宸紙RMSD锛夈€佽鐩栫巼鍜屽簭鍒楀悓涓€鎬у垎鏋愩€?/p>

鐮旂┒涓娇鐢ㄧ殑鏁版嵁闆?/h2>

1. 璁粌鍜岄獙璇侀泦锛氫娇鐢ㄤ簡 PDBBind 閫氱敤闆嗙殑涓嶅悓鐗堟湰锛岃€冭檻浜嗗簭鍒楀悓涓€鎬у拰鍒嗗瓙鍔涘鑳介噺鏈€灏忓寲绛夋爣鍑嗐€?/li>
2. Astex 澶氭牱鍖栭泦锛歅DB 涓鏍峰寲銆侀珮璐ㄩ噺鐨勮泲鐧借川-閰嶄綋澶嶅悎鐗╅泦鍚堛€?/li>
3. PoseBusters 鍩哄噯闆?/strong>锛氶珮璐ㄩ噺鐨勮泲鐧借川-閰嶄綋澶嶅悎鐗╂柊闆嗗悎锛屽寘鍚嵂鐗╂牱鍒嗗瓙锛岄€夊彇浜嗗鏍锋€у拰鐩稿叧鎬с€?/li>

涓昏缁撴灉姒傝

• 馃寠 Astex 澶氭牱鎬ч泦涓婄殑缁撴灉锛氬熀浜庢繁搴﹀涔狅紙DL-based锛夌殑鏂规硶鍦ㄥ叾宸茶缁冪殑澶嶅悎鐗╀笂琛ㄧ幇鑹ソ锛屼絾鐗╃悊鍚堢悊鎬ф湁寰呮彁楂樸€?/li>
• 馃悮 PoseBusters 鍩哄噯闆嗕笂鐨勭粨鏋?/strong>锛氭墍鏈夋柟娉曞湪 PoseBusters 鍩哄噯闆嗕笂鐨勮〃鐜颁笉濡?Astex 澶氭牱鎬ч泦锛屽嚫鏄惧嚭娉涘寲鑳藉姏鐨勯噸瑕佹€с€?/li>
• 鈿欙笍 鏋勮薄瀵规帴鑳介噺鏈€灏忓寲缁撴灉锛氶€氳繃棰濆鐨勮兘閲忔渶灏忓寲姝ラ锛屽彲浠ユ敼鍠勫熀浜庢繁搴﹀涔犵殑鏂规硶鐨勭墿鐞嗗悎鐞嗘€с€?/li>

Astex 澶氭牱鎬ч泦鏄瘎浼板垎瀛愬鎺ユ柟娉曠殑甯哥敤鍩哄噯銆傚湪杩欎釜鏁版嵁闆嗕笂锛屼竷绉嶆柟娉曪紙鍖呮嫭 AutoDock Vina銆丟old銆丏eepDock 绛夛級鐨勮〃鐜伴€氳繃 RMSD锛堝潎鏂规牴鍋忓樊锛夎鐩栫巼灞曠幇銆傚熀浜庢繁搴﹀涔犵殑鏂规硶鍦ㄨ繖浜涘鍚堢墿涓婄殑琛ㄧ幇棰勬湡杈冨ソ锛屽洜涓哄畠浠ぇ澶氳缁冧簬姝ゃ€傜劧鑰岋紝浠庣墿鐞嗗悎鐞嗘€ц搴﹁€冭檻锛岃澶氬熀浜庢繁搴﹀涔犵殑鏂规硶鐨勯娴嬭〃鐜颁笉灏戒汉鎰忋€備緥濡傦紝DiffDock 鍦?RMSD 涓婅〃鐜板嚭鑹诧紝浣嗗湪鐗╃悊鍚堢悊鎬ф柟闈㈠垯杈冧负閫婅壊銆?/p>

鍦?PoseBusters 鍩哄噯闆嗕笂锛屾墍鏈夋柟娉曠殑琛ㄧ幇鏅亶涓嬮檷锛屽嚫鏄惧嚭鏂规硶娉涘寲鑳藉姏鐨勯噸瑕佹€с€傚湪鏈€冭檻鐗╃悊鍚堢悊鎬х殑鎯呭喌涓嬶紝浼犵粺鏂规硶濡?Gold 鍜?AutoDock Vina 鐨勮〃鐜颁緷鏃т紭寮傘€傜劧鑰岋紝鍩轰簬娣卞害瀛︿範鐨勬柟娉曞湪鐗╃悊鍚堢悊鎬ф柟闈㈣〃鐜颁笉浣筹紝鐗瑰埆鏄湪棰勬祴绔嬩綋鍖栧鍜屾纭殑閿暱鏂归潰銆?/p>

杩涗竴姝ョ殑鍒嗘瀽鏄剧ず锛屽鍩轰簬娣卞害瀛︿範鐨勬柟娉曠敓鎴愮殑鏋勮薄杩涜棰濆鐨勫垎瀛愬鎺ヨ兘閲忔渶灏忓寲澶勭悊锛屽彲浠ユ彁楂樺叾鐗╃悊鍚堢悊鎬с€傝繖琛ㄦ槑灏界鍩轰簬娣卞害瀛︿範鐨勬柟娉曞湪鍒濆棰勬祴涓彲鑳藉瓨鍦ㄧ己闄凤紝浣嗛€氳繃鍚庡鐞嗘楠わ紝瀹冧滑鐨勮緭鍑哄彲浠ヨ浼樺寲锛屼粠鑰屽湪瀹為檯搴旂敤涓洿涓烘湁鏁堛€?/p>

鍥捐〃涓€锛氬鎺ユ柟娉曠殑姣旇緝鎬ц兘鍒嗘瀽

璇ュ浘琛ㄥ睍绀轰簡鍦ㄤ袱涓祴璇曢泦涓婂悇绉嶅鎺ユ柟娉曠殑姣旇緝鎬ц兘銆傞€夋嫨浜?Astex 澶氭牱鎬ч泦锛堝寘鍚?85 涓渚嬶級浣滀负鏄撲簬娴嬭瘯鐨勯泦鍚堬紝鍏朵腑鍖呮嫭澶氫釜缁忎簲绉嶅熀浜庢繁搴﹀涔狅紙DL锛夌殑鏂规硶璁粌鐨勫鍚堢墿銆?/p>

鑰?PoseBusters 鍩哄噯娴嬭瘯闆嗭紙鍖呭惈 308 涓渚嬶級鍒欎綔涓洪毦搴﹁緝楂樼殑娴嬭瘯闆嗭紝鍥犱负鍏朵腑鐨勫鍚堢墿鍧囨湭缁忎换浣曟祴璇曟柟娉曡缁冦€傚浘涓潯绾归儴鍒嗗睍绀轰簡姣忕鏂规硶棰勬祴缁撴灉涓潎鏂规牴鍋忓樊锛圧MSD锛夊湪 2脜 浠ュ唴鐨勬瘮渚嬶紝瀹炲績閮ㄥ垎鍒欏睍绀轰簡鍚屾椂鍏锋湁鏈夋晥鍑犱綍缁撴瀯鍜岃兘閲忕殑棰勬祴缁撴灉锛屽嵆閫氳繃鎵€鏈?PoseBusters 娴嬭瘯涓旇瑙嗕负銆孭B-鏈夋晥銆嶇殑銆?/p>

浠?Astex 澶氭牱鎬ч泦鐨勭粨鍚堟ā寮?RMSD 鏉ョ湅锛堟潯绾硅摑缁胯壊閮ㄥ垎锛夛紝DiffDock 鍦ㄤ紶缁熸柟娉曚腑琛ㄧ幇绐佸嚭銆傜劧鑰岋紝鍦ㄥ悓鏃惰€冭檻鐗╃悊鍚堢悊鎬э紙瀹炲績钃濈豢鑹查儴鍒嗭級鎴栭潰瀵?PoseBusters 鍩哄噯娴嬭瘯闆嗭紙鐝婄憵鑹查儴鍒嗭級鏃讹紝AutoDock Vina 鍜?Gold 鍦ㄦ墍鏈夊熀浜?DL 鐨勬柟娉曚腑琛ㄧ幇鏈€浣炽€?/p>

鍥捐〃浜岋細Astex 澶氭牱鎬ф暟鎹泦涓?TankBind 棰勬祴鐨勭€戝竷鍥?/h3>

姝ゅ浘琛ㄥ睍绀轰簡 TankBind 棰勬祴鍦?Astex 澶氭牱鎬ф暟鎹泦涓婄殑绛涢€夋晥鏋滐紝浠?PoseBusters 娴嬭瘯浣滀负璇勪及鏍囧噯銆?/p>

PoseBusters 娴嬭瘯濂椾欢鍦ㄤ笅鏂囪〃 4 涓湁璇︾粏鎻忚堪銆傛渶宸︿晶鐨勮櫄绾挎煴浠ｈ〃娴嬭瘯闆嗕腑鐨勫鍚堢墿鎬绘暟銆傜孩鑹叉煴浣撳睍绀轰簡闅忕潃娴嬭瘯澧炲姞锛屼粠宸﹁嚦鍙抽娴嬪け璐ョ殑鏁伴噺澧炲姞銆傛渶鍙充晶鐨勫疄蹇冩煴浣撲唬琛ㄩ€氳繃鎵€鏈夋祴璇曠殑棰勬祴鏁伴噺锛屽嵆琚涓烘槸銆孭B-鏈夋晥銆嶇殑棰勬祴銆?/p>

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鍥捐〃鍥涳細鍩轰簬 PoseBusters 鍩哄噯娴嬭瘯闆?/h3>

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鍩轰簬 DL 鐨勬柟娉曞湪涓庡叾璁粌闆嗙浉浼肩殑铔嬬櫧璐ㄤ笂琛ㄧ幇鏇翠匠銆?/p>

鍥捐〃浜旓細瀵规帴鏂规硶鍦?PoseBusters 鍩哄噯娴嬭瘯闆嗕笂鐨勬瘮杈冩€ц兘

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鏉＄汗鏌变綋鏄剧ず浜嗘瘡绉嶆柟娉曚腑鍏锋湁鏅朵綋鏋勮薄 2脜 鍐?RMSD 鐨勯娴嬫瘮渚嬶紝瀹炲績鏌变綋鏄剧ず浜嗘澶栭€氳繃鎵€鏈?PoseBusters 娴嬭瘯鐨勯娴嬶紝鍥犳琚涓烘槸 PB-鏈夋晥鐨勩€傚悗瀵规帴鑳介噺鏈€灏忓寲鏄捐憲鎻愰珮浜嗗熀浜?DL 鏂规硶棰勬祴鐨勭浉瀵圭墿鐞嗗悎鐞嗘€с€?/p>

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鍥捐〃鍏細鍚庡鎺ヨ兘閲忔渶灏忓寲淇鐨勯娴嬬ず渚?/h3>

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Uni-Mol 鐨勯娴嬬粨鏋滐紙2.0 脜锛変互鐧借壊鏄剧ず锛屼紭鍖栧悗鐨勯娴嬶紙1.1 脜锛変互绮夎壊鏄剧ず锛岃€屽弬鑰冪殑鏅朵綋閰嶄綋鍒欎互娴呰摑鑹茶〃绀恒€?/p>

鍙互娉ㄦ剰鍒帮紝鍦ㄤ紭鍖栬繃绋嬩腑鑺抽鐜鍘嬪钩锛屾渶宸︿晶鐨勯敭闀垮害涔熻缂╃煭锛屼娇寰楅娴嬮€氳繃浜嗘墍鏈?PoseBusters 鐨勬鏌ャ€?/p>

琛ㄦ牸 1锛氭繁搴﹀涔犲鎺ユ柟娉曠殑绮鹃€夋渚?/h3>

琛ㄦ牸 2锛氳缁冩繁搴﹀涔犲鎺ユ柟娉曠殑鏁版嵁闆嗛€夋嫨

闃愯堪浜嗚繖浜旂鍩轰簬鏈哄櫒瀛︿範鐨勫鎺ユ柟娉曟墍鐢ㄧ殑璁粌鏁版嵁闆嗐€傝繖浜涙柟娉曢兘鏄湪 PDBBind 2020 閫氱敤闆嗙殑瀛愰泦涓婃帴鍙楄缁冪殑銆?/p>

琛ㄦ牸 3锛氬簲鐢ㄥ鎺ユ柟娉曠殑鎼滅储绌洪棿浠嬬粛

琛ㄦ牸 4锛歅oseBusters 娴嬭瘯濂椾欢鐨勬鏌ユ弿杩?/h3>

璁ㄨ

• 馃К 瀵规瘮浼犵粺鏂规硶鍜屽熀浜?DL 鐨勬柟娉?/li>
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• 馃洜锔?鎻ず鍩轰簬 DL 鐨勬柟娉曠殑灞€闄愭€?/li>

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PoseBusters 娴嬭瘯濂椾欢涓殑涓埆娴嬭瘯鍑告樉浜嗕竴浜涘鎺ョ浉鍏崇殑澶辫触妯″紡銆備緥濡傦紝Uni-Mol 棰勬祴浜嗛潪鏍囧噯鐨勯敭闀匡紝鑰?TankBind 閫犳垚浜嗛厤浣撳唴閮ㄥ啿绐併€傝瘑鍒繖浜涘け璐ユā寮忓浜庡紑鍙戣€呮敼杩涚粨鍚堟ā寮忛娴嬫柟娉曞拰鎻愰珮棰勬祴鐨勫噯纭€у拰鐜板疄鎬ц嚦鍏抽噸瑕併€?/p>

姝ゅ锛屼笌浼犵粺鏂规硶涓嶅悓锛屽熀浜?DL 鐨勬柟娉曞湪鏂版暟鎹笂鐨勬硾鍖栬兘鍔涜緝寮便€傝繖浜涙柟娉曞湪 PoseBusters 鍩哄噯娴嬭瘯闆嗕笂鏁翠綋琛ㄧ幇涓嶄匠锛屽湪搴忓垪鍚屼竴鎬ц緝浣庣殑 PoseBusters 瀛愰泦涓婂鏄撹繃鎷熷悎銆傛垜浠搴忓垪鍚屼竴鎬т綆浜?30%鐨勯澏鏍囧垎鏋愬彂鐜帮紝鍑犱箮鎵€鏈夊熀浜?DL 鐨勬柟娉曢兘鏈兘鍦?2 脜 闃堝€煎唴鐢熸垚鐗╃悊涓婃湁鏁堢殑鏋勮薄銆?/p>

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鍗充娇鍦ㄨ繘琛岄厤浣撶殑鑳介噺鏈€灏忓寲姝ラ鍚庯紝琛ㄧ幇鏈€浣崇殑鍩轰簬 DL 鐨勬柟娉?DiffDock 涔熸湭鑳借秴瓒婁紶缁熸柟娉曞 Gold 鍜?AutoDock Vina銆傝繖琛ㄦ槑锛屽湪鍔涘満涓紪鐮佺殑鏌愪簺鍏抽敭鍖栧鍜岀墿鐞嗘柟闈㈠彲鑳界己澶变簬娣卞害瀛︿範妯″瀷涓€?/p>

PoseBusters 娴嬭瘯濂椾欢鎻愪緵浜嗕竴涓柊鏍囧噯锛孭B 鏈夋晥鎬э紝瓒呰秺浜嗕紶缁熺殑銆孯MSD銆嶃€?/p>鍙傝€冭祫鏂?

• Buttenschoen, M., Morris, G. M., & Deane, C. M. (2024). PoseBusters: AI-based docking Methods fail to generate physically valid poses or generalise to novel sequences. Chemical Science. https://doi.org/10.1039/d3sc04185a

• Data and code:聽https://github.com/maabuu/posebusters

• PDF Download: https://is.gd/nsG1sG

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